[gmx-users] sridhar-problem with Position Restrained Dynamics run.

Mr.Sridhar sridhar at www.cdfd.org.in
Sat Apr 26 23:35:01 CEST 2003


Dear GMX users,

I am running dynamics of a KINASE protein. It contains two zinc ions and a
Phorbol residue for which i could generate topology using PRODRG server.
I ran smoothly till minimization. I created .tpr file by grompp for
position restrained dynamics. But when I ran mdrun the program crashed
giving some message which I could not get.

I am attaching the logfile and input mdp files. I'll be grateful to you if
anyone of you can send me suggessions.

regards,

sridhar

-------------- next part --------------
[sridhar at einstein PTR_WT]$ mdrun -s b4pr_PTR.tpr -o pr_PTR.trr -c pr_PTR.gro -e pr_PTR.edr -g pr_PTR.log
                         :-)  G  R  O  M  A  C  S  (-:

           Glycine aRginine prOline Methionine Alanine Cystine Serine

                            :-)  VERSION 3.1.4  (-:


       Copyright (c) 1991-2002, University of Groningen, The Netherlands
         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                                :-)  mdrun  (-:

Option     Filename  Type          Description
------------------------------------------------------------
  -s   b4pr_PTR.tpr  Input         Generic run input: tpr tpb tpa
  -o     pr_PTR.trr  Output        Full precision trajectory: trr trj
  -x       traj.xtc  Output, Opt.  Compressed trajectory (portable xdr format)
  -c     pr_PTR.gro  Output        Generic structure: gro g96 pdb
  -e     pr_PTR.edr  Output        Generic energy: edr ene
  -g     pr_PTR.log  Output        Log file
-dgdl      dgdl.xvg  Output, Opt.  xvgr/xmgr file
-table    table.xvg  Input, Opt.   xvgr/xmgr file
-rerun    rerun.xtc  Input, Opt.   Generic trajectory: xtc trr trj gro g96 pdb
 -ei        sam.edi  Input, Opt.   ED sampling input
 -eo        sam.edo  Output, Opt.  ED sampling output
  -j       wham.gct  Input, Opt.   General coupling stuff
 -jo        bam.gct  Input, Opt.   General coupling stuff
-ffout      gct.xvg  Output, Opt.  xvgr/xmgr file
-devout   deviatie.xvg  Output, Opt.  xvgr/xmgr file
-runav  runaver.xvg  Output, Opt.  xvgr/xmgr file
 -pi       pull.ppa  Input, Opt.   Pull parameters
 -po    pullout.ppa  Output, Opt.  Pull parameters
 -pd       pull.pdo  Output, Opt.  Pull data output
 -pn       pull.ndx  Input, Opt.   Index file
-mtx         nm.mtx  Output, Opt.  Hessian matrix

      Option   Type  Value  Description
------------------------------------------------------
      -[no]h   bool     no  Print help info and quit
      -[no]X   bool     no  Use dialog box GUI to edit command line options
       -nice    int     19  Set the nicelevel
     -deffnm string         Set the default filename for all file options
         -np    int      1  Number of nodes, must be the same as used for
                            grompp
      -[no]v   bool     no  Be loud and noisy
-[no]compact   bool    yes  Write a compact log file
  -[no]multi   bool     no  Do multiple simulations in parallel (only with -np
                            > 1)
   -[no]glas   bool     no  Do glass simulation with special long range
                            corrections
 -[no]ionize   bool     no  Do a simulation including the effect of an X-Ray
                            bombardment on your system

Reading file b4pr_PTR.tpr, VERSION 3.1.4 (single precision)
Reading file b4pr_PTR.tpr, VERSION 3.1.4 (single precision)
starting mdrun 'PROTEIN in water'
12500 steps,     25.0 ps.


Step 23, time 0.046 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.181315 (between atoms 544 and 545) rms 0.016906
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 24, time 0.048 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.187019 (between atoms 544 and 545) rms 0.017486
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 25, time 0.05 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.192341 (between atoms 544 and 545) rms 0.018013
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 26, time 0.052 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.198004 (between atoms 544 and 545) rms 0.018558
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 27, time 0.054 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.204713 (between atoms 544 and 545) rms 0.019227
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 28, time 0.056 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.212396 (between atoms 544 and 545) rms 0.020056
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 29, time 0.058 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.220131 (between atoms 544 and 545) rms 0.020974
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 30, time 0.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.226986 (between atoms 544 and 545) rms 0.021867
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 31, time 0.062 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.232960 (between atoms 544 and 545) rms 0.022692
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 32, time 0.064 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.238841 (between atoms 544 and 545) rms 0.023522
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 33, time 0.066 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.245276 (between atoms 544 and 545) rms 0.024465
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 34, time 0.068 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.252222 (between atoms 544 and 545) rms 0.025560
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 35, time 0.07 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.258983 (between atoms 544 and 545) rms 0.026746
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 36, time 0.072 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.264623 (between atoms 544 and 545) rms 0.027886
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 37, time 0.074 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.268473 (between atoms 544 and 545) rms 0.028841
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 38, time 0.076 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.270573 (between atoms 544 and 545) rms 0.029539
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 39, time 0.078 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.276367 (between atoms 545 and 547) rms 0.030066
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 40, time 0.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.288514 (between atoms 545 and 547) rms 0.030688
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 41, time 0.082 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.307101 (between atoms 545 and 546) rms 0.031753
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 42, time 0.084 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.337229 (between atoms 545 and 546) rms 0.033491
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 43, time 0.086 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.376150 (between atoms 545 and 546) rms 0.035872
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 44, time 0.088 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.423276 (between atoms 545 and 546) rms 0.038846
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 45, time 0.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.486992 (between atoms 545 and 546) rms 0.043006
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 46, time 0.092 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.601741 (between atoms 545 and 546) rms 0.050495
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 47, time 0.094 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.968486 (between atoms 545 and 546) rms 0.071379
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    545    546  108.8    0.0609   0.0048      0.1530

Step 48, time 0.096 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.335241 (between atoms 543 and 544) rms 0.023874
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    545    546   49.0    0.0048   0.1609      0.1530
    545    547   35.0    0.0374   0.1407      0.1530

Step 49, time 0.098 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 1.059695 (between atoms 545 and 548) rms 0.089588
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    543    544   84.9    0.0951   0.1000      0.1430
    544    545   72.9    0.1559   0.2114      0.1390
    544    548   54.3    0.1569   0.3007      0.1530
    544    570   85.9    0.1075   0.1469      0.1530
    545    546   91.7    0.1609   0.3055      0.1530
    545    547   73.1    0.1407   0.2550      0.1530
    545    548   76.7    0.1447   0.3151      0.1530
    548    549   44.1    0.1239   0.1531      0.1530

Step 50, time 0.1 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 408.580536 (between atoms 544 and 570) rms 40.039604
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    540    541   46.7    0.1485   1.1800      0.1530
    541    542   70.2    0.1238   1.2836      0.1250
    541    543   95.6    0.1341  10.1273      0.1360
    543    544  170.9    0.1000  15.9260      0.1430
    544    545  111.2    0.2114  41.4304      0.1390
    544    548  121.3    0.3007  16.4072      0.1530
    544    570  108.7    0.1469  62.6658      0.1530
    545    546   80.9    0.3055  48.0758      0.1530
    545    547   89.8    0.2550  46.3930      0.1530
    545    548   99.6    0.3151  51.6299      0.1530
    548    549   94.6    0.1531  22.8949      0.1530
    549    550   98.3    0.1553   5.0037      0.1530
    549    565   92.5    0.1503  11.3127      0.1530
    550    551   95.0    0.1374   0.1775      0.1390
    555    556  102.5    0.1533   0.9265      0.1530
    556    557  103.7    0.1362   0.8716      0.1360
    556    559  102.2    0.1392   0.8829      0.1390
    556    564  107.3    0.1537   3.3983      0.1530
    557    558  129.6    0.1000   0.0110      0.1000
    561    563   96.7    0.1331   0.7199      0.1330
    563    564  102.0    0.1535   3.6064      0.1530
    564    565  100.3    0.1551   7.9435      0.1530
    565    566   96.0    0.1370   9.4886      0.1360
    565    568   94.9    0.1546  32.3286      0.1530
    566    567   95.2    0.1002   1.9018      0.1000
    568    569   95.9    0.1526  23.9389      0.1530
    568    570   88.8    0.1639  18.4868      0.1530
    570    571   82.8    0.1506  35.6715      0.1430
    571    572  105.1    0.0971   6.6537      0.1000
Warning: 1-4 interaction at distance larger than 1
These are ignored for the rest of the simulation
turn on -debug for more information

Step 51, time 0.102 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 44678.804688 (between atoms 556 and 559) rms 3882.019287
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    543    544  137.3   15.9282 107.7693      0.1430
    544    545  171.8   41.4359 418.0484      0.1390
    544    548  152.4   16.4094 103.5373      0.1530
    544    570  116.8   62.6742 115.5157      0.1530
    545    546  165.6   48.0822 449.8415      0.1530
    545    547  153.5   46.3992 448.0979      0.1530
    545    548  168.3   51.6367 474.2516      0.1530
    548    549  100.7   22.8980 153.6293      0.1530
    549    550   85.1    5.0043 210.7006      0.1530
    549    565  145.1   11.3142 361.5642      0.1530
    550    551  175.6    0.1775 642.7932      0.1390
    551    552  160.1    0.1520 566.7393      0.1530
    551    555   38.8    0.1235 1832.9689      0.1530
    552    553   50.1    0.1469 136.9207      0.1430
    553    554  139.9    0.1003  17.4599      0.1000
    555    556  167.7    0.9266 5484.2695      0.1530
    556    557  173.7    0.8717 5241.3574      0.1360
    556    559  167.5    0.8831 6210.4927      0.1390
    556    564   46.4    3.3988 4453.8042      0.1530
    557    558   48.6    0.0110 1489.0624      0.1000
    559    560  137.9    0.0995 2513.2668      0.1230
    561    562  167.8    0.1404 1269.4021      0.1530
    561    563  162.7    0.7200 1452.3428      0.1330
    564    565  141.1    7.9446 1074.5206      0.1530
    565    566  155.8    9.4899 381.2719      0.1360
    565    568  110.5   32.3329 346.8463      0.1530
    566    567   74.3    1.9021  49.5390      0.1000
    568    569  111.2   23.9421  45.0886      0.1530
    568    570  145.1   18.4892  44.1936      0.1530
    570    571  139.5   35.6762  51.2577      0.1430
    571    572   33.2    6.6546  15.2466      0.1000
Wrote pdb files with previous and current coordinates

Step 51  Warning: pressure scaling more than 1%, mu: 11.5075 11.5075 11.5075
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]
-------------- next part --------------
;
;	User sridhar
;	POSITION RESTRAINED DYNAMICS - PTR
;
title               =  PTR
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  12500	; total 25 ps.
nstcomm             =  1
nstxout             =  500
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  0.9
fourierspacing      =  0.12
fourier_nx	    =  0
fourier_ny	    =  0
fourier_nz	    =  0
pme_order	    =  4
ewald_rtol	    =  1e-5
optimize_fft	    =  yes
; Berendsen temperature coupling is on in three groups
Tcoupl              =  berendsen
tc-grps		    =  protein	ZN  DRG  sol  CL
tau_t               =  0.1	0.1 0.1  0.1  0.1
ref_t               =  300      300 300  300  300
; Energy monitoring
energygrps	    =  protein	ZN DRG sol  CL
; Pressure coupling is not on
Pcoupl              =  berendsen
pcoupltype          =  isotropic 
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529


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