[gmx-users] methane in water

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Sun Jan 24 23:47:24 CET 2010


Hello,

    I am running rdf simulations, and I tried running simple methane  
using OPLS-AA force-field for 100ns. I was hoping to get a smoother  
curve for such a small molecule in 100ns. Could someone please look  
over my mdp parameters and suggest if I am missing something.

Thanks.


Nisha Patel

-------------- next part --------------
; RUN CONTROL PARAMETERS =
integrator               = sd
; start time and timestep in ps =
tinit                    = 0
dt                       = 0.002
nsteps                   = 50000000
; number of steps for center of mass motion removal =
nstcomm                  = 100
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 100000
nstvout                  = 100000
nstfout                  = 0
; Output frequency for energies to log file and energy file =
nstlog                   = 100000
nstenergy                = 500
; Output frequency and precision for xtc file =
nstxtcout                = 10000
xtc-precision            = 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
;xtc_grps                 = 
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 10
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or none =
pbc                      = xyz
; nblist cut-off         =
rlist                    = 1.0
domain-decomposition     = no 
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = pme-switch
;rcoulomb-switch          = 0.9
rcoulomb                  = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r                = 1
; Method for doing Van der Waals =
vdw-type                 = switch
; cut-off lengths        =
rvdw-switch              = 0.8
rvdw                     = 0.9
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                  = EnerPres
; Spacing for the PME/PPPM FFT grid =
fourierspacing           = 0.1
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters =
pme_order                = 6
ewald_rtol               = 1e-06
epsilon_surface          = 0
optimize_fft             = no
;restraints
dihre= yes
dihre-fc=1
nstdihreout=1000
disre= Simple
disre_fc=1 
;OPTIONS FOR TEMPERATURE COUPLING
tc_grps                  = system
tau_t                    = 2.0
ref_t                    = 300
;OPTIONS FOR PRESSURE COUPLING
Pcoupl                   = Isotropic
tau_p                    = 1.0
compressibility          = 4.5e-05
ref_p                    = 1.0 
; Free energy control stuff
free_energy              = yes
init_lambda              = 0.0
delta_lambda             = 0
sc_alpha                 =0.5
sc-power                 =1.0
sc-sigma                 = 0.3 
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 171533

; OPTIONS FOR BONDS     =
constraints              = all-bonds
; Type of constraint algorithm =
constraint-algorithm     = Lincs
; Do not constrain the start configuration =
unconstrained-start      = no
; Relative tolerance of shake =
shake-tol                = 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order              = 12
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle          = 30

-------------- next part --------------
;
;	File 'topol.top' was generated
;	By user: user (1000)
;	On host: Tigrans-Lab
;	At date: Fri Jan 22 13:54:29 2010
;
;	This is your topology file
;	methane pair in water
;
; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
Methane            3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
     1   opls_138      1   METH      C      1      -0.24     12.011   ; qtot -0.24
     2   opls_140      1   METH    HC1      1       0.06      1.008   ; qtot -0.18
     3   opls_140      1   METH    HC2      1       0.06      1.008   ; qtot -0.12
     4   opls_140      1   METH    HC3      1       0.06      1.008   ; qtot -0.06
     5   opls_140      1   METH    HC4      1       0.06      1.008   ; qtot 0

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1 
    1     3     1 
    1     4     1 
    1     5     1 

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    2     1     3     1 
    2     1     4     1 
    2     1     5     1 
    3     1     4     1 
    3     1     5     1 
    4     1     5     1 

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif


[ system ]
; Name
methane pair in water

[ molecules ]
; Compound        #mols
Methane             1
SOL               897
-------------- next part --------------
# This file was created Sun Jan 24 17:02:57 2010
# by the following command:
# g_rdf -f traj.xtc -s topol.tpr -n index.ndx -o methwater100ns.xvg -rdf mol_com 
#
# g_rdf is part of G R O M A C S:
#
# GROup of MAchos and Cynical Suckers
#
@    title "Radial distribution of molecule COM"
@    xaxis  label "r"
@    yaxis  label ""
@TYPE xy
@ subtitle "METH - OW"
         0          0
     0.002          0
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       0.1          0
     0.102          0
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       0.2          0
     0.202          0
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     0.256          0
     0.258          0
      0.26          0
     0.262          0
     0.264 0.00344476
     0.266          0
     0.268          0
      0.27          0
     0.272          0
     0.274          0
     0.276          0
     0.278 0.00310653
      0.28 0.00306232
     0.282          0
     0.284 0.00297667
     0.286 0.00880565
     0.288  0.0173673
      0.29  0.0199834
     0.292  0.0225264
     0.294  0.0638851
     0.296  0.0411031
     0.298  0.0838099
       0.3   0.125378
     0.302   0.136887
     0.304   0.189645
     0.306   0.189739
     0.308   0.253084
      0.31   0.299796
     0.312   0.355155
     0.314   0.487009
     0.316   0.521747
     0.318    0.61491
      0.32   0.614282
     0.322   0.694668
     0.324   0.827912
     0.326   0.817788
     0.328    0.99307
      0.33   0.959021
     0.332    1.06732
     0.334    1.11266
     0.336    1.30361
     0.338    1.33026
      0.34    1.36243
     0.342    1.46149
     0.344    1.57439
     0.346    1.59637
     0.348    1.56022
      0.35    1.71294
     0.352    1.70709
     0.354    1.69745
     0.356    1.83376
     0.358    1.82832
      0.36    1.78767
     0.362    1.98603
     0.364     1.8084
     0.366    1.86576
     0.368    1.87213
      0.37    1.75022
     0.372    1.76616
     0.374    1.83657
     0.376    1.80522
     0.378    1.75926
      0.38    1.72582
     0.382    1.74564
     0.384    1.76659
     0.386    1.87239
     0.388    1.61712
      0.39    1.70476
     0.392    1.63118
     0.394    1.63166
     0.396     1.6841
     0.398    1.66571
       0.4    1.47353
     0.402    1.57478
     0.404    1.62543
     0.406    1.50315
     0.408    1.49419
      0.41    1.43252
     0.412    1.49927
     0.414     1.4568
     0.416    1.39149
     0.418    1.44417
      0.42    1.36512
     0.422    1.35762
     0.424    1.32746
     0.426    1.34546
     0.428    1.29753
      0.43    1.20627
     0.432    1.20028
     0.434    1.21856
     0.436     1.2049
     0.438    1.13759
      0.44    1.11982
     0.442    1.13552
     0.444    1.15333
     0.446    1.08627
     0.448    1.07899
      0.45    1.14649
     0.452    1.06234
     0.454    1.07046
     0.456   0.996435
     0.458    1.01636
      0.46    1.02116
     0.462   0.983095
     0.464    0.95791
     0.466    1.05475
     0.468    0.95147
      0.47   0.966214
     0.472   0.972057
     0.474   0.968138
     0.476   0.990756
     0.478   0.953056
      0.48   0.863855
     0.482   0.895982
     0.484   0.900874
     0.486   0.869084
     0.488   0.892219
      0.49    0.84795
     0.492   0.865872
     0.494   0.842146
     0.496   0.844158
     0.498   0.836417
       0.5    0.86238
     0.502   0.810768
     0.504   0.806232
     0.506   0.811107
     0.508   0.838249
      0.51   0.851044
     0.512   0.804132
     0.514   0.808772
     0.516   0.831388
     0.518   0.817801
      0.52   0.831968
     0.522   0.773624
     0.524   0.809674
     0.526   0.771445
     0.528   0.825006
      0.53   0.829932
     0.532   0.833004
     0.534    0.77545
     0.536   0.815633
     0.538   0.775544
      0.54   0.759132
     0.542    0.78866
     0.544   0.811292
     0.546   0.809361
     0.548     0.7835
      0.55    0.78813
     0.552   0.846228
     0.554   0.861275
     0.556   0.788274
     0.558   0.808106
      0.56   0.805381
     0.562   0.780675
     0.564   0.857428
     0.566   0.824368
     0.568   0.815616
      0.57   0.823184
     0.572   0.851216
     0.574   0.823413
     0.576    0.91542
     0.578   0.873852
      0.58   0.851448
     0.582   0.843486
     0.584   0.922861
     0.586   0.936179
     0.588   0.897854
      0.59   0.916634
     0.592   0.935771
     0.594   0.939027
     0.596   0.955725
     0.598   0.925142
       0.6    0.97103
     0.602    1.02617
     0.604     1.0023
     0.606    1.01071
     0.608    1.03267
      0.61    1.03237
     0.612     1.0147
     0.614    1.02597
     0.616    1.01801
     0.618    1.01084
      0.62     1.0449
     0.622   0.997254
     0.624    1.00014
     0.626    1.10092
     0.628    1.02457
      0.63    1.04043
     0.632    1.05251
     0.634    1.04823
     0.636    1.04585
     0.638    1.06286
      0.64    1.06856
     0.642    1.07706
     0.644    1.03042
     0.646    1.09367
     0.648     1.0669
      0.65    1.14334
     0.652     1.0674
     0.654    1.05193
     0.656    1.11025
     0.658     1.0641
      0.66    1.04613
     0.662    1.06553
     0.664    1.08202
     0.666    1.04844
     0.668    1.04058
      0.67    1.02797
     0.672    1.06807
     0.674    1.01316
     0.676    1.05547
     0.678    1.06183
      0.68     1.0784
     0.682    1.03702
     0.684    1.03041
     0.686    1.05558
     0.688    1.07023
      0.69     1.0388
     0.692     1.0579
     0.694    1.03084
     0.696    1.02992
     0.698    1.08361
       0.7    1.03093
     0.702    1.02603
     0.704     1.0008
     0.706    1.06452
     0.708    1.04892
      0.71    1.03351
     0.712    1.03148
     0.714    1.03797
     0.716    1.03126
     0.718    1.00733
      0.72    1.04808
     0.722    1.00448
     0.724    1.02371
     0.726    1.03535
     0.728    1.05734
      0.73    1.03218
     0.732    1.02203
     0.734    1.02229
     0.736    1.02026
     0.738    1.02137
      0.74    1.04259
     0.742    1.00211
     0.744    1.00495
     0.746    1.03022
     0.748     1.0406
      0.75    1.00899
     0.752   0.982856
     0.754     1.0473
     0.756    1.00483
     0.758   0.989055
      0.76   0.998853
     0.762    1.01553
     0.764    1.00196
     0.766    1.02337
     0.768    1.04243
      0.77   0.986438
     0.772    0.96801
     0.774    1.01875
     0.776    1.03026
     0.778   0.988833
      0.78   0.996829
     0.782    1.03763
     0.784    1.03513
     0.786   0.989791
     0.788    1.02501
      0.79   0.999451
     0.792   0.987865
     0.794    1.01378
     0.796    1.00487
     0.798   0.972713
       0.8    1.02223
     0.802    1.00037
     0.804    1.00205
     0.806    1.02558
     0.808   0.982249
      0.81    1.02313
     0.812    1.01884
     0.814   0.980127
     0.816    1.01105
     0.818   0.988866
      0.82   0.995492
     0.822   0.976443
     0.824    0.98618
     0.826    0.98038
     0.828   0.974918
      0.83    1.01731
     0.832   0.971128
     0.834   0.974086
     0.836    1.02234
     0.838   0.965467
      0.84   0.968057
     0.842   0.996958
     0.844    1.00641
     0.846    0.98386
     0.848   0.973576
      0.85   0.971991
     0.852   0.958145
     0.854   0.979373
     0.856   0.974758
     0.858   0.987872
      0.86    1.01376
     0.862    0.99133
     0.864   0.991531
     0.866     1.0062
     0.868   0.955356
      0.87   0.999798
     0.872   0.988917
     0.874   0.997574
     0.876   0.973975
     0.878   0.987568
      0.88   0.991797
     0.882   0.994717
     0.884    1.01139
     0.886    1.00043
     0.888    1.01356
      0.89   0.997518
     0.892   0.982462
     0.894   0.996725
     0.896    1.00843
     0.898   0.986944
       0.9    0.99711
     0.902   0.998571
     0.904    1.00917
     0.906   0.994457
     0.908    0.99301
      0.91     0.9895
     0.912   0.996169
     0.914    1.01451
     0.916   0.994033
     0.918   0.989451
      0.92   0.999582
     0.922    1.02043
     0.924   0.972674
     0.926    1.00071
     0.928    1.01647
      0.93   0.984032
     0.932    0.99229
     0.934   0.981126
     0.936   0.985741
     0.938    1.01017
      0.94   0.996391
     0.942    1.00109
     0.944   0.981202
     0.946   0.996131
     0.948    1.01621
      0.95    1.00878
     0.952    1.01326
     0.954    1.01062
     0.956    1.00037
     0.958    1.01341
      0.96   0.990483
     0.962    0.96869
     0.964   0.990024
     0.966   0.994388
     0.968    1.00006
      0.97   0.989524
     0.972    1.01064
     0.974   0.994094
     0.976   0.995288
     0.978    1.00506
      0.98   0.985687
     0.982     1.0031
     0.984    1.00223
     0.986     1.0019
     0.988   0.985802
      0.99    1.00066
     0.992    1.00201
     0.994    1.00307
     0.996    1.01625
     0.998    1.00517
         1    1.02206
     1.002    1.01752
     1.004    1.01058
     1.006    1.02266
     1.008    1.00638
      1.01    1.01958
     1.012    1.00594
     1.014   0.993041
     1.016    1.01619
     1.018    1.02099
      1.02    1.00314
     1.022    1.00175
     1.024    1.02526
     1.026   0.992129
     1.028   0.998715
      1.03    1.02156
     1.032    0.99708
     1.034   0.992496
     1.036    1.02252
     1.038    1.01588
      1.04    1.01378
     1.042    1.03901
     1.044    1.03839
     1.046   0.996248
     1.048   0.997035
      1.05    1.00391
     1.052    1.01935
     1.054   0.995022
     1.056    1.01816
     1.058    1.01581
      1.06   0.984142
     1.062    1.00266
     1.064    1.00736
     1.066     1.0135
     1.068    1.00994
      1.07    1.02099
     1.072   0.987359
     1.074    0.99432
     1.076    1.00346
     1.078    1.01608
      1.08    1.00998
     1.082   0.995053
     1.084   0.992993
     1.086    1.00891
     1.088   0.988495
      1.09     1.0017
     1.092    1.00852
     1.094    1.00463
     1.096    1.01475
     1.098    1.00204
       1.1   0.978217
     1.102    1.00373
     1.104    1.01959
     1.106   0.985503
     1.108    1.03996
      1.11    0.99399
     1.112    1.00207
     1.114   0.995777
     1.116    1.01295
     1.118    0.98424
      1.12    1.00063
     1.122   0.982388
     1.124    1.00662
     1.126    0.99922
     1.128   0.979883
      1.13   0.994468
     1.132   0.993587
     1.134    1.00832
     1.136    1.02622
     1.138    1.01298
      1.14    1.01108
     1.142    1.00534
     1.144    1.00929
     1.146   0.999256
     1.148   0.989217
      1.15   0.983967
     1.152    1.00931
     1.154    1.00971
     1.156   0.987257
     1.158    1.01624
      1.16    1.00026
     1.162   0.988044
     1.164    1.00704
     1.166   0.997236
     1.168   0.972164
      1.17    1.01411
     1.172    1.00201
     1.174    1.01905
     1.176    1.01194
     1.178    1.00193
      1.18    1.02382
     1.182   0.985373
     1.184   0.980497
     1.186   0.984872
     1.188   0.990408
      1.19    1.00347
     1.192   0.966702
     1.194    1.00305
     1.196    1.00138
     1.198   0.991335
       1.2    1.00865
     1.202    0.99174
     1.204    1.04242
     1.206    1.00465
     1.208    1.02479
      1.21   0.988168
     1.212    1.00959
     1.214     1.0053
     1.216    1.01189
     1.218    1.00334
      1.22   0.972839
     1.222   0.984305
     1.224   0.990372
     1.226    1.01328
     1.228    1.00496
      1.23    1.01279
     1.232    1.00287
     1.234   0.964459
     1.236    0.99946
     1.238    1.00664
      1.24    1.00308
     1.242    1.00329
     1.244    1.02239
     1.246   0.999734
     1.248    1.01214
      1.25   0.997392
     1.252   0.995761
     1.254   0.992798
     1.256    1.00859
     1.258   0.995512
      1.26    1.00704
     1.262   0.998875
     1.264    1.00602
     1.266     1.0008
     1.268    1.00749
      1.27    0.98573
     1.272   0.997471
     1.274    1.00212
     1.276    1.01039
     1.278   0.984604
      1.28   0.997059
     1.282   0.982634
     1.284    1.01911
     1.286   0.996191
     1.288    1.01277
      1.29   0.985995
     1.292    1.00932
     1.294   0.999418
     1.296    0.98987
     1.298    1.01477
       1.3    1.00706
     1.302    1.00286
     1.304   0.989082
     1.306    1.00223
     1.308   0.999306
      1.31   0.991154
     1.312    1.01164
     1.314    1.00189
     1.316   0.995793
     1.318    1.01364
      1.32    1.01795
     1.322    1.01549
     1.324    1.01558
     1.326    0.98969
     1.328    1.00722
      1.33   0.996118
     1.332    1.00435
     1.334   0.975983
     1.336    1.00644
     1.338    0.99892
      1.34   0.998681
     1.342    1.00651
     1.344   0.988623
     1.346    1.00512
     1.348   0.997426
      1.35    1.00172
     1.352    1.00061
     1.354    1.00917
     1.356    1.01396
     1.358    1.01028
      1.36    1.01457
     1.362    1.00666
     1.364    1.00824
     1.366    1.01282
     1.368   0.996709
      1.37    1.00251
     1.372    1.00685
     1.374   0.987447
     1.376    1.01976
     1.378    1.01114
      1.38    0.98462
     1.382    1.00364
     1.384    1.01998
     1.386    1.02374
     1.388    1.02501
      1.39    1.00381
     1.392   0.992367
     1.394   0.978979
     1.396    1.01354
     1.398     0.9964
       1.4   0.988542
     1.402    1.01117
     1.404    1.00142
     1.406    1.00441
     1.408    1.00411
      1.41   0.998593
     1.412    1.01449
     1.414    1.00413
     1.416    0.98356
     1.418    1.00205
      1.42   0.993806
     1.422    1.00949
     1.424    1.00391
     1.426    1.01326
     1.428    1.00278
      1.43    1.00813
     1.432    1.00387
     1.434    1.01144
     1.436   0.986279
     1.438    1.01662
      1.44   0.985272
     1.442    1.01677
     1.444   0.988741
     1.446    1.01116
     1.448    1.00016
      1.45   0.988237
     1.452    1.00155
     1.454    1.00937
     1.456   0.995389
     1.458    1.00977
      1.46    1.01178
     1.462    1.02306
     1.464   0.986344
     1.466    1.01083
     1.468   0.992992
      1.47   0.996622
     1.472    1.00103
     1.474    1.00657
     1.476    1.00446
     1.478   0.993675
      1.48   0.983097
     1.482    1.01259
     1.484     1.0057


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