[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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