wiki:fmt

File Formats


inputConstr

The 'inputConstr' provides structural constraints. For example, the disulfide bond information. This can also be used to fix part of the structure. The file is produced by 'findSS' and consumed by 'complex'.

An example inputConstr is as follows, showing the CYS 6 to CYS 127 bond:

AtomPair         1.6.SG          1.127.SG        1.96    2.04
AtomPair         1.6.CB          1.127.SG        2.95    3.06
AtomPair         1.6.SG          1.127.CB        2.95    3.06
AtomPair         1.6.CA          1.127.SG        2.0     3.364   1.0     4.094   -1.0    7.5
AtomPair         1.6.SG          1.127.CA        2.0     3.364   1.0     4.094   -1.0    7.5
AtomPair         1.6.CB          1.127.CB        2.0     3.520   1.2     4.075   -1.2    7.5
<snip>

Here is a constraint file example which "fixes" part of the structure:

# fix residues 5 thru 20 of the 1st chain
Static           1.5-20.*
# fix the CA atoms of chains 2 thru 3
Static           2-3.*.CA

Here is the xDMDConst file which explains the layout:

###############################################
#       XDMD Constraint input file            #
###############################################
# Keywords: AtomPair, BasePair, Static, Harmonic
#
#
#
#Format: AtomPair AtomSelect#1 AtomSelect#2 Pot
#*AtomSelect: ChainIndex.ResidueIndex.AtomPDBName
#--ChainIndex  : For any complex, first chain's index start from 1
#--ResidueIndex: For each chain, first residue's index start from 1
#--AtomPDBName : The atom's pdb name
#*Pot: defined according to DMD/xDMD's potential
#
#
#Format: BasePair BaseSelect#1 BaseSelect#2
#*BaseSelect: ChainIndex.ResidueIndex
#
#
#Format: Static AtomSelections
#*AtomSelections: ChainIDs.ResidueIndexes.AtomPDBNames
#--Here, the syntax of IDs, Inexes, and Names follow a simple rule:
#---1. no space in-between, seperated by ","
#---2. '-'seperate two integers to define a conscutive set of ints
#---3. '*' is wild-cast to define every chain, residues, or every atoms
#For example:
#   *.*.N         (Atom N of all residues@all chains)
#   1-2.*.N,CA    (Atoms N,CA of all residues@chains 1 to 2
#   1-2,4.12,19.* (All atoms of residues 12 and 19@chain 1,2,4
#   1.1-4.CA      (Atom CA of residues 1 to 4@chain 1)
#
#
#Format: Harmonic AtomSelections K
#*AtomSelections: ChainIDs.ResidueIndexes.AtomPDBNames
#--Here, K is the spring constant
#
####################################################################
#
#Example of Some special geometry
#
##Disulfide Bond (Ci, Cj: chain Index; Ri,Rj: Residue Index)
#AtomPair       Ci.Ri.SG                Cj.Rj.SG 1.96    2.04
#AtomPair       Ci.Ri.CB                Cj.Rj.SG 2.95    3.06
#AtomPair       Ci.Ri.SG                Cj.Rj.CB 2.95    3.06
#AtomPair       Ci.Ri.CA                Cj.Rj.SG 2.0     3.364   1.0     4.094   -1.0    7.5
#AtomPair       Ci.Ri.CB                Cj.Rj.CB 2.0     3.520   1.2     4.075   -1.2    7.5
#AtomPair       Ci.Ri.SG                Cj.Rj.CA 2.0     3.364   1.0     4.094   -1.0    7.5
#
#Peptide Bond
#AtomPair       Ci.Ri.C                 Cj.Rj.N  1.302   1.356
#AtomPair       Ci.Ri.CA                Cj.Rj.N  2.391   2.459
#AtomPair       Ci.Ri.O                 Cj.Rj.N  2.219   2.281
#AtomPair       Ci.Ri.C                 Cj.Rj.HN 1.980   2.060
#AtomPair       Ci.Ri.C                 Cj.Rj.CA 2.401   2.469
#AtomPair       Ci.Ri.CB                Cj.Rj.N  2.650   2.700 0.100 2.750 0.100 2.800 0.100 2.850 0.100 2.900 0.100 2.950 1.000 4.000
#AtomPair       Ci.Ri.CA                Cj.Rj.CA 3.773   3.887
#AtomPair       Ci.Ri.C                 Cj.Rj.CB 2.940   4.060
#AtomPair       Ci.Ri.C                 Cj.Rj.C  2.700   2.846 1.500 2.910 0.500 4.00
#AtomPair       Ci.Ri.O                 Cj.Rj.HN 3.113   3.207
#AtomPair       Ci.Ri.O                 Cj.Rj.CA 2.600   2.788
##2nd atom is Proline
#AtomPair       Ci.Ri.CB                Cj.Rj.N  2.950   4.050
#AtomPair       Ci.Ri.CA                Cj.Rj.CA 2.871   2.989 -2.00 3.773 2.00 3.887
#AtomPair       Ci.Ri.O                 Cj.Rj.CA 2.600   2.788 -2.00 3.475 2.00 3.765
#AtomPair       Ci.Ri.CA                Cj.Rj.CD 2.811   3.039 -2.00 3.677 2.00 3.983
#AtomPair       Ci.Ri.C                 Cj.Rj.CD 2.453   2.559
#AtomPair       Ci.Ri.O                 Cj.Rj.CD 2.560   3.840
#AtomPair       Ci.Ri.C                 Cj.Rj.CB 3.200   4.800
#
#
#Harmonic constraint
#Harmonic       1.*.*   1.0
#

.param

The '.param' file contains several text sections described below. It is produced by 'complex' and consumed by 'xDMD' and 'rexDMD'.

The .param file contains title headers followed by line separated lists of detail as follows:

  • NUMBER OF ATOMS
    • The number of atoms to simulate
    • Contains:
      • Number of atoms (Integer)
  • ATOM TYPES
    • Lists the unique atoms types to simulate
    • Contains:
      • Assigned atom type number (Integer)
      • Mass [from !paramDir files] (Float)
      • Radius [from ParamDir files] (Float)
  • NON-BONDED POTENTIALS
    • Lists the potentials between all pairs of ATOM TYPES
    • Contains:
      • Assigned atom type number 1 (Integer)
      • Assigned atom type number 2 (Integer)
      • 23 separate potential parameters (Float)
  • REACTION POTENTIALS
    • Lists the potentials between some pairs (the reactive ones) of ATOM TYPES
    • Contains:
      • Assigned atom type number 1 (Integer)
      • Assigned atom type number 2 (Integer)
      • Varying number of separate reaction potential parameters (Float)
  • REACTIONS
    • Lists reaction control parameters (?) between some pairs (quads?) of ATOM TYPES
    • Contains:
      • Assigned atom type number 1 (Integer)
      • Assigned atom type number 2 (Integer)
      • ? Assigned atom type number 3 (Integer)
      • ? Assigned atom type number 4 (Integer)
      • ? 4 additional fields
  • REACTION LIST
    • Lists reactions possible between triples (?) of atoms (not ATOM TYPES)
    • Contains:
      • Atom number 1 (Integer)
      • Atom number 2 (Integer)
      • Atom number 3 (Integer)
  • BONDED POTENTIALS
    • Lists potential parameters for bonds (?)
    • Contains:
      • ? (Integer)
      • ? 6 to ?? separate potential parameters (Float)
  • CONNECTIVITIES
    • Lists connections among triples of atoms
    • Contains:
      • Atom number 1 (Integer)
      • Atom number 2 (Integer)
      • Atom number 3 (Integer)

A snipped example of 1HEL.param:

NUMBER OF ATOMS
1269
ATOM TYPES
1 12.000000 1.000000
2 12.000000 1.055000
<snip>
105 16.000000 1.290000
NON-BONDED POTENTIALS
1 1   0.1000   0.2900   1.0000   0.4800   1.0000   0.6700   1.0000   0.8600   1.0000   1.0500   1.0000   1.2400   1.0000   1.4300   1.0000   1.6200   1.0000   1.8100   1.0000   2.0000  10.0000   2.1000   0.2000
2 1   0.1000   0.2900   1.0000   0.4800   1.0000   0.6700   1.0000   0.8600   1.0000   1.0500   1.0000   1.2400   1.0000   1.4300   1.0000   1.6200   1.0000   1.8100   1.0000   2.0000  10.0000   2.5000   0.2000
<snip>
105 104   0.1000   0.3480   1.0000   0.5960   1.0000   0.8440   1.0000   1.0920   1.0000   1.3400   1.0000   1.5880   1.0000   1.8360   1.0000   2.0840   1.0000   2.3320   1.0000   2.5800  10.0000   2.7100   0.5156   2.9850   0.2193   3.\6100  -0.0759   6.5000  -0.0153
105 105   0.1000   0.3480   1.0000   0.5960   1.0000   0.8440   1.0000   1.0920   1.0000   1.3400   1.0000   1.5880   1.0000   1.8360   1.0000   2.0840   1.0000   2.3320   1.0000   2.5800  10.0000   2.7100   0.5156   2.9850   0.2193   3.\6100  -0.0759   6.5000  -0.0153
REACTION POTENTIALS
86 87 1.760000 2.200000 -0.600000 2.500001 -0.600000
86 10 2.750000 2.870000 0.600000 3.280000 -0.600000 3.800000 -10.000000 3.990000 10.600000 4.000000
<snip>
91 105 1.740000 1.820000 0.600000 2.530000 -0.600000 3.000001 -1.000000
26 105 2.680000 2.770000 1.000000 3.350000 -0.500000 3.550000 -0.500000 4.000000 -10.000000 4.990000 11.000000 5.000000
REACTIONS
1 15 86 87 1 2.5 0 5
1 19 86 88 1 2.5 0 5
<snip>
1 50 86 105 1 3 0 5
24 50 91 105 1 3 0 5
REACTION LIST
2 0 1
11 1 10
<snip>
1262 256 1261
1265 257 1264
BONDED POTENTIALS
1     0.10000  0.60000  1.00000  0.62000  1.00000  0.64000  1.00000  0.66000  1.00000  0.68000  1.00000  0.70000  1.00000  0.72000  1.00000  0.74000  1.00000  0.76000  1.00000  0.78000  1.00000  0.80000  1.00000  0.82000  1.00000  0.8400\0  1.00000  0.86000  1.00000  0.88000  1.00000  0.90000  1.00000  0.92000  1.00000  0.94000  1.00000  0.96000  1.00000  0.98000 20.00000  1.02000 -20.00000  1.27000 -1.00000  1.52000 -1.00000  1.77000 -1.00000  2.02000 -1.00000  2.27000 \-1.00000  2.52000 -1.00000  2.77000 -1.00000  3.02000 -1.00000  3.27000 -1.00000  3.52000 -1.00000  3.77000 -1.00000  4.02000 -1.00000  4.27000 -1.00000  4.52000 -1.00000  4.77000 -1.00000  5.02000 -1.00000  5.27000 -1.00000  5.52000 -1.\00000  5.77000 -1.00000  7.49998 -10000.00000  7.49999  10039.00000  7.50000
2     0.10000  0.87480  1.00000  0.90396  1.00000  0.93312  1.00000  0.96228  1.00000  0.99144  1.00000  1.02060  1.00000  1.04976  1.00000  1.07892  1.00000  1.10808  1.00000  1.13724  1.00000  1.16640  1.00000  1.19556  1.00000  1.2247\2  1.00000  1.25388  1.00000  1.28304  1.00000  1.31220  1.00000  1.34136  1.00000  1.37052  1.00000  1.39968  1.00000  1.42884 20.00000  1.48716 -20.00000  1.73716 -1.00000  1.98716 -1.00000  2.23716 -1.00000  2.48716 -1.00000  2.73716 \-1.00000  2.98716 -1.00000  3.23716 -1.00000  3.48716 -1.00000  3.73716 -1.00000  3.98716 -1.00000  4.23716 -1.00000  4.48716 -1.00000  4.73716 -1.00000  4.98716 -1.00000  5.23716 -1.00000  5.48716 -1.00000  5.73716 -1.00000  5.98716 -1.\00000  6.23716 -1.00000  7.49998 -10000.00000  7.49999  10039.00000  7.50000
<snip>
344   0.01000  2.00000 10.00000  2.80000  0.60000  7.50000
345   0.01000  3.00000 10.00000  3.70000  0.60000  7.50000
CONNECTIVITIES
10 11 1
10 12 1
<snip>
1264 1267 18
1263 1269 18

.state

The .state file contains information about the status of the system. It is produced by 'complex' and is consumed by 'xDMD'.

The .state file contains title headers followed by line separated lists of detail as follows:

After running 'complex' the .state file will contain the following sections:

  • DIMENSION
    • This is the size of the box
    • Contains:
      • x dimension (Float)
      • Y dimension (Float)
      • z dimension (Float)
  • ATOMS
    • This is list of the atom states
    • Contains:
      • Atom number (Integer)
      • Assigned atom type (Integer)
      • x,y,z coordinates (Float)
      • x,y,z velocity (Float)
      • ChainID (Integer)
      • ResidueID (Integer)
      • isSideChain (boolean)

A snipped example of 1HEL.state:

DIMENSION
    500.00000     500.00000     500.00000
ATOMS
#Format: AtomIndex AtomType Displacement Velocity [chainID [residueID [isSideChain]]]
     1   26  253.7238270077667  239.5689097862806  241.0351815838176   -0.7114677521237   -0.0441577911618    1.5706263439484 1 1
     2   24  254.3895698382225  240.5862663402885  241.5571997952066   -0.4865637085327   -1.3191926226545    1.8311895079348 1 1
<snip>
  1268    5  237.1218270077667  251.7199097862806  238.9191815838176    1.0202415568533   -0.8847969760086   -0.9642896434307 1 129
  1269    5  237.4598270077667  249.2729097862806  239.2031815838176   -0.1932940751844    0.4986536822899    0.7380783976570 1 129

.const

The constraint file .const contains a list of atom constraints. It is produce by 'complex' and consumed by 'xDMD' and 'rexDMD'.

After running 'complex' the constraint file 1HEL.const will contain a list of constraints:

  • Atom number 1 (Integer)
  • Atom number 2 (Integer)
  • A variable number of constraint parameters (Float)

An example 1HEL.const:

    62   1242 1.960000 2.040000
    61   1242 2.950000 3.060000
    62   1241 2.950000 3.060000
    58   1242 2.000000 3.364000 1.000000 4.094000 -1.000000 7.500000
    62   1238 2.000000 3.364000 1.000000 4.094000 -1.000000 7.500000
    61   1241 2.000000 3.520000 1.200000 4.075000 -1.200000 7.500000
   299   1125 1.960000 2.040000 -20.000000 2.048274 -1.000000 2.056548 -1.000000 2.064823 -1.000000 2.073097 -1.000000 2.081371 -1.000000 2.089645 -1.000000 2.097919 -1.000000 2.106194 -1.000000 2.114468 -1.000000 2.122742 -1.000000 2.13\1016 -1.000000 2.139291 -1.000000 2.147565 -1.000000 2.155839 -1.000000 2.164113 -1.000000 2.172387 -1.000000 2.180662 -1.000000 2.188936 -1.000000 2.197210 -1.000000 2.205284 -10000.000000 2.205384 10039.000000 2.205484
   298   1125 2.950000 3.060000 -20.000000 3.068744 -1.000000 3.077487 -1.000000 3.086231 -1.000000 3.094974 -1.000000 3.103718 -1.000000 3.112461 -1.000000 3.121205 -1.000000 3.129948 -1.000000 3.138692 -1.000000 3.147435 -1.000000 3.15\6179 -1.000000 3.164922 -1.000000 3.173666 -1.000000 3.182409 -1.000000 3.191153 -1.000000 3.199896 -1.000000 3.208640 -1.000000 3.217383 -1.000000 3.226127 -1.000000 3.234670 -10000.000000 3.234770 10039.000000 3.234870
   299   1124 2.950000 3.060000 -20.000000 3.066846 -1.000000 3.073692 -1.000000 3.080538 -1.000000 3.087383 -1.000000 3.094229 -1.000000 3.101075 -1.000000 3.107921 -1.000000 3.114767 -1.000000 3.121613 -1.000000 3.128458 -1.000000 3.13\5304 -1.000000 3.142150 -1.000000 3.148996 -1.000000 3.155842 -1.000000 3.162688 -1.000000 3.169533 -1.000000 3.176379 -1.000000 3.183225 -1.000000 3.190071 -1.000000 3.196717 -10000.000000 3.196817 10039.000000 3.196917
   295   1125 2.000000 3.364000 1.000000 4.094000 -1.000000 7.500000
   299   1121 2.000000 3.364000 1.000000 4.094000 -1.000000 7.500000
   298   1124 2.000000 3.520000 1.200000 4.075000 -1.200000 7.500000
   646    797 1.960000 2.040000
   645    797 2.950000 3.060000
   646    796 2.950000 3.060000
   642    797 2.000000 3.364000 1.000000 4.094000 -1.000000 7.500000
   646    793 2.000000 3.364000 1.000000 4.094000 -1.000000 7.500000
   645    796 2.000000 3.520000 1.200000 4.075000 -1.200000 7.500000
   762    913 1.960000 2.040000 -20.000000 2.047734 -1.000000 2.055468 -1.000000 2.063203 -1.000000 2.070937 -1.000000 2.078671 -1.000000 2.086405 -1.000000 2.094139 -1.000000 2.101874 -1.000000 2.109608 -1.000000 2.117342 -1.000000 2.12\5076 -1.000000 2.132810 -1.000000 2.140545 -1.000000 2.148279 -1.000000 2.156013 -1.000000 2.163747 -1.000000 2.171481 -1.000000 2.179216 -1.000000 2.186950 -1.000000 2.194484 -10000.000000 2.194584 10039.000000 2.194684
   761    913 2.950000 3.060000
   762    912 2.950000 3.060000 -20.000000 3.066167 -1.000000 3.072335 -1.000000 3.078502 -1.000000 3.084670 -1.000000 3.090837 -1.000000 3.097004 -1.000000 3.103172 -1.000000 3.109339 -1.000000 3.115506 -1.000000 3.121674 -1.000000 3.12\7841 -1.000000 3.134009 -1.000000 3.140176 -1.000000 3.146343 -1.000000 3.152511 -1.000000 3.158678 -1.000000 3.164845 -1.000000 3.171013 -1.000000 3.177180 -1.000000 3.183148 -10000.000000 3.183248 10039.000000 3.183348
   758    913 2.000000 3.364000 1.000000 4.094000 -1.000000 7.500000
   762    909 2.000000 3.364000 1.000000 4.094000 -1.000000 7.500000
   761    912 2.000000 3.520000 1.200000 4.075000 -1.200000 7.500000

.task

The task file defines the temperature, the thermostat parameter, and the length of the simulation.

  • The temperature unit is kcal/mol/kB. For example, 0.6 in DMD is approximiately 300 Kelvin.
  • The time unit is approximately 50fs.

The task file is used for relaxation and simulation runs.

Here is an example relax.task for a relaxation run:

#THIS IS THE EXAMPLE INPUT FILE FOR xDMD SIMULATIONS.
#THE COMMENT LINE starts with the 1st non whitespace character as "#" or"//".
#
#THERMOSTAT: ANDERSON or BERENDSON, right now BERENDSON is not implemented yet
#
#T_NEW is the instant temperature at the moment of simulation. If specified, the
# velocities of input state/restart willbe re-scaled
#
#T_LIMIT is the targeting temprature
#
#HEAT_X_C determines how often the exchange takes place betwen IMAGINARY
# solvent and system atoms: dT = 1/HEAT_X_C.
#
THERMOSTAT              ANDERSON
T_NEW                   0.7
T_LIMIT                 0.7
HEAT_X_C                10.0


#
#RESTART_FILE specifies the name of the OUTPUT restart file, DEFAULT "dmd_restart"
#
#RESTART_DT specifies the delta-time to save each restart file, the file will be
# overwritten, DEFAULT 1000
#
RESTART_FILE            relax.dmd_restart
RESTART_DT              10


#
#ECHO_FILE specifies the name of the output file to write the output
# parameters(energy,pressure,tempeature etc.)
#
#ECHO_DT specifies the delta-time to save the output parameters
#
ECHO_FILE               relax.dmd_echo
ECHO_DT                 0.1


#
#MOVIE_FILE specifies the movie output file
#
#MOVIE_DT specifies the delta time to save the snapshort
#
#MOVIE_SAVE_START specifies the starting atom to be saved, DEFAULT 1
#
#MOVIE_SAVE_END specifies the endinig atom to be saveed, DEAULT the last atom in the system
#if you has no idea of the system, PLEASE do not specify MOVIE_SAVE_START and MOVIE_SAVE_END
#
MOVIE_FILE              relax.dmd_movie
MOVIE_DT                10
#MOVIE_SAVE_START       1
#MOVIE_SAVE_END         100


#
#START_TIME specifies the initial time when the simulation starts, DEFAULT 0
#
#MAX_TIME specifies the maximum time for the simulation to last
#
START_TIME              0
MAX_TIME                100

And here is an example task file for an equilibrium run:

#THIS IS THE EXAMPLE INPUT FILE FOR xDMD SIMULATIONS.
#THE COMMENT LINE starts with the 1st non whitespace character as "#" or"//".
#
#THERMOSTAT: ANDERSON or BERENDSON, right now BERENDSON is not implemented yet
#
#T_NEW is the instant temperature at the moment of simulation. If specified, the
# velocities of input state/restart willbe re-scaled
#
#T_LIMIT is the targeting temprature
#
#HEAT_X_C determines how often the exchange takes place betwen IMAGINARY
# solvent and system atoms: dT = 1/HEAT_X_C.
#
THERMOSTAT              ANDERSON
T_NEW                   0.60
T_LIMIT                 0.60
HEAT_X_C                0.1


#
#RESTART_FILE specifies the name of the OUTPUT restart file, DEFAULT "dmd_restart"
#
#RESTART_DT specifies the delta-time to save each restart file, the file will be
# overwritten, DEFAULT 1000
#
RESTART_FILE            equi.dmd_restart
RESTART_DT              100


#
#ECHO_FILE specifies the name of the output file to write the output
# parameters(energy,pressure,tempeature etc.)
#
#ECHO_DT specifies the delta-time to save the output parameters
#
ECHO_FILE               equi.dmd_echo
ECHO_DT                 10


#
#MOVIE_FILE specifies the movie output file
#
#MOVIE_DT specifies the delta time to save the snapshort
#
#MOVIE_SAVE_START specifies the starting atom to be saved, DEFAULT 1
#
#MOVIE_SAVE_END specifies the endinig atom to be saveed, DEAULT the last atom in the system
#if you has no idea of the system, PLEASE do not specify MOVIE_SAVE_START and MOVIE_SAVE_END
#
MOVIE_FILE              equi.dmd_movie
MOVIE_DT                100
#MOVIE_SAVE_START       1
#MOVIE_SAVE_END         100


#
#START_TIME specifies the initial time when the simulation starts, DEFAULT 0
#
#MAX_TIME specifies the maximum time for the simulation to last
#
START_TIME              0
MAX_TIME                10000

.dmd_echo

The .dmd_echo are text files produced by xDMD and can be used as input to a spreadsheet program or simple text reader.

They have a text format and contain:

  • Time, temperature, pressure, average & instantaneous potential energy, and instanteous kinetic energy
  • Filename is defined in taskFile

Here is a example:

#ave = average; inst = instant
#Time         aveTemperature          avePressure       avePotential   instPotential    instKineticE
      10.000         0.52932         0.0000009973          -95.50041      -147.93100      1039.15633
      20.000         0.54737         0.0000001523         -167.72709      -229.43530      1069.23457
<snip>
Last modified 8 years ago Last modified on Nov 10, 2010 1:15:50 PM