[gmx-users] countinuation run problem
Anthony Cruz
acb15885 at uprm.edu
Thu Feb 23 20:39:23 CET 2006
On Thursday 23 February 2006 5:51 am, David van der Spoel wrote:
> Anthony Cruz wrote:
> > HI:
> > Yesterday one of my simulation crash. I check the log file. This are the
> > last lines of the file:
> >
> > Step Time Lambda
> > 6109000 12218.00098 0.00000
> >
> > Rel. Constraint Deviation: Max between atoms RMS
> > Before LINCS 0.058792 1139 1140 0.007195
> > After LINCS 0.000126 75 77 0.000021
> >
> > Energies (kJ/mol)
> > G96Angle Proper Dih. Improper Dih. LJ-14
> > Coulomb-14 3.95784e+03 1.69609e+03 1.21916e+03 7.85820e+02
> > 3.20988e+04 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
> > Potential 2.49591e+05 -7.40570e+03 -1.58839e+06 -2.16905e+05
> > -1.52336e+06 Kinetic En. Total Energy Temperature Pressure (bar)
> > 2.74080e+05 -1.24927e+06 2.97765e+02 -8.69934e+00
> >
> > Then I try to use tpbconvert to continue the simulation by the following
> > command:
> >
> > -bash-2.05b$ tpbconv -f 1scnMD_MV.trr -e 1scn_MD_ENER.edr -s
> > 1scn_MD_TPR.tpr -o 1scn_MD_TPR_CONT.tpr
> >
> > :-) G R O M A C S (-:
> >
> > Grunge ROck MAChoS
> >
> > :-) VERSION 3.2.1 (-:
> >
> > Written by David van der Spoel, Erik Lindahl, Berk Hess, and
> > others. Copyright (c) 1991-2000, University of Groningen, The
> > Netherlands. Copyright (c) 2001-2004, The GROMACS development team, check
> > out http://www.gromacs.org for more information.
> >
> > 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.
> >
> > :-) tpbconv (-:
> >
> > Option Filename Type Description
> > ------------------------------------------------------------
> > -s 1scn_MD_TPR.tpr Input Generic run input: tpr tpb tpa xml
> > -f 1scnMD_MV.trr Input, Opt! Full precision trajectory: trr trj
> > -e 1scn_MD_ENER.edr Input, Opt! Generic energy: edr ene
> > -n index.ndx Input, Opt. Index file
> > -o 1scn_MD_TPR_CONT.tpr Output Generic run input: tpr tpb tpa
> > xml
> >
> > 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 0 Set the nicelevel
> > -time real -1 Continue from frame at this time (ps) instead
> > of the last frame
> > -extend real 0 Extend runtime by this amount (ps)
> > -until real 0 Extend runtime until this ending time (ps)
> > -[no]zeroq bool no Set the charges of a group (from the index)
> > to zero
> > -[no]unconstrained
> > bool yes For a continuous trajectory, the constraints
> > should not be solved before the first step
> > (default)
> >
> > Reading toplogy and shit from 1scn_MD_TPR.tpr
> > Reading file 1scn_MD_TPR.tpr, VERSION 3.2.1 (single precision)
> > Modifying ir->bUncStart to TRUE
> >
> > READING COORDS, VELS AND BOX FROM TRAJECTORY 1scnMD_MV.trr...
> >
> > trn version: GMX_trn_file (single precision)
> > Read frame 2334: step 1166500 time 2333.000
> >
> > Using frame of step 1166500 time 2333
> > Opened 1scn_MD_ENER.edr as single precision energy file
> > Reading frame 2330 time 2330.000
> >
> > READ 3 PRESSURE COUPLING MU'S FROM 1scn_MD_ENER.edr
> >
> >
> > READ 4 TEMPERATURE COUPLING LAMBDAS FROM 1scn_MD_ENER.edr
> >
> > 10083500 steps (20167 ps) remaining from first run.
> > Writing statusfile with starting step 1166500 and length 10083500
> > steps...
> > time 2333.000 and length 20167.000 ps
> >
> > Back Off! I just backed up 1scn_MD_TPR_CONT.tpr to
> > ./#1scn_MD_TPR_CONT.tpr.1#
> >
> > gcq#162: "Rub It Right Accross Your Eyes" (F. Zappa)
> >
> >
> > The total time of my simulation is 22ns and as the log file said it runs
> > for Step Time Lambda
> > 6109000 12218.00098 0.00000
> > but tpbconv use time 2333.000 and length 20167.000 ps for the
> > continue file. The output control in my mdp file are the fallowing:
> >
> > ; Output Control
> > nstxout = 500
> > nstvout = 500
> > nstfout = 0
> > nstlog = 500
> > nstenergy = 500
> >
> >
> > What is wrong? Why do not continue at the last frame described in the
> > log file??
> >
> > Best regards
> > Anthony
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> run gmxcheck on your edr and trr files. Sometimes the OS buffers these
> files.
>
> maybe you have a full disk.
I run the gmxcheck and this is the oputput whe I use the trr file:
-bash-2.05b$ gmxcheck -f 1scnMD_MV.trr -c 1scn_MD_TPR.tpr -e 1scn_MD_ENER.edr
>output
Option Filename Type Description
------------------------------------------------------------
-f 1scnMD_MV.trr Input, Opt! Generic trajectory: xtc trr trj gro g96 pdb
-f2 traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb
-s1 top1.tpr Input, Opt. Generic run input: tpr tpb tpa xml
-s2 top2.tpr Input, Opt. Generic run input: tpr tpb tpa xml
-c 1scn_MD_TPR.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96
pdb xml
-e 1scn_MD_ENER.edr Input, Opt! Generic energy: edr ene
-e2 ener2.edr Input, Opt. Generic energy: edr ene
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 0 Set the nicelevel
-vdwfac real 0.8 Fraction of sum of VdW radii used as warning
cutoff
-bonlo real 0.4 Min. fract. of sum of VdW radii for bonded atoms
-bonhi real 0.7 Max. fract. of sum of VdW radii for bonded atoms
-tol real 0 Relative tolerance for comparing real values
defined as 2*(a-b)/(|a|+|b|)
-lastener string Last energy term to compare (if not given all are
tested). It makes sense to go up until the
Pressure.
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
# Atoms 110722
Last frame 2333 time 2333.000
Item #frames Timestep (ps)
Step 2334 1
Time 2334 1
Lambda 2334 1
Coords 2334 1
Velocities 2334 1
Forces 0
Box 2334 1
Checking energy file 1scn_MD_ENER.edr
Opened 1scn_MD_ENER.edr as single precision energy file
frame: 0 (index 0), t: 0.000
Reading frame 12210 time 12210.001
Last frame read 12217
WARNING: Incomplete frame: nr 12218 time 12217.001
Found 12217 frames with a timestep of 1 ps.
Checking coordinate file 1scn_MD_TPR.tpr
Reading file 1scn_MD_TPR.tpr, VERSION 3.2.1 (single precision)
Reading file 1scn_MD_TPR.tpr, VERSION 3.2.1 (single precision)
110722 atoms in file
coordinates found
box found
velocities found
Kinetic energy: 411498 (kJ/mol)
Assuming the number of degrees of freedom to be Natoms * 3 or Natoms * 2,
the velocities correspond to a temperature of the system
of 297.993 K or 446.99 K respectively.
Checking for atoms closer than 0.8 and not between 0.4 and 0.7,
relative to sum of Van der Waals distance:
Opening library file /usr/local/gromacs/share/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/top/atommass.dat
Opening library file /usr/local/gromacs/share/top/vdwradii.dat
Opening library file /usr/local/gromacs/share/top/dgsolv.dat
atom# name residue r_vdw atom# name residue r_vdw distance
39 CA PRO 5 0.15 41 CG PRO 5 0.15 0.2354
50 CD1 TYR 6 0.15 52 CD2 TYR 6 0.15 0.2392
54 CE1 TYR 6 0.15 56 CE2 TYR 6 0.15 0.2398
72 CG1 ILE 8 0.15 73 CG2 ILE 8 0.15 0.2366
78 CA PRO 9 0.15 80 CG PRO 9 0.15 0.236
191 CD1 PHE 21 0.15 193 CD2 PHE 21 0.15 0.2399
191 CD1 PHE 21 0.15 199 CZ PHE 21 0.15 0.2372
193 CD2 PHE 21 0.15 199 CZ PHE 21 0.15 0.2378
242 CG1 VAL 26 0.15 243 CG2 VAL 26 0.15 0.2307
263 CG1 VAL 28 0.15 264 CG2 VAL 28 0.15 0.2362
352 CG HISB 39 0.15 355 CE1 HISB 39 0.15 0.2161
354 CD2 HISB 39 0.15 355 CE1 HISB 39 0.15 0.2176
381 CD1 LEU 42 0.15 382 CD2 LEU 42 0.15 0.2381
415 C GLY 46 0.15 419 CA GLY 47 0.15 0.2385
441 CD1 PHE 50 0.15 443 CD2 PHE 50 0.15 0.2366
441 CD1 PHE 50 0.15 449 CZ PHE 50 0.15 0.2359
443 CD2 PHE 50 0.15 449 CZ PHE 50 0.15 0.2365
493 CD1 TYR 56 0.15 495 CD2 TYR 56 0.15 0.235
497 CE1 TYR 56 0.15 499 CE2 TYR 56 0.15 0.2387
560 CG HISA 63 0.15 564 CE1 HISA 63 0.15 0.2189
563 CD2 HISA 63 0.15 564 CE1 HISA 63 0.15 0.2187
586 CG HISB 66 0.15 589 CE1 HISB 66 0.15 0.2114
588 CD2 HISB 66 0.15 589 CE1 HISB 66 0.15 0.215
732 CB PRO 85 0.15 734 CD PRO 85 0.15 0.233
774 CG TYR 90 0.15 781 CE2 TYR 90 0.15 0.2377
775 CD1 TYR 90 0.15 783 CZ TYR 90 0.15 0.2344
777 CD2 TYR 90 0.15 783 CZ TYR 90 0.15 0.2392
846 CB SER 97 0.15 849 C SER 97 0.15 0.2389
889 CG TYR 103 0.15 894 CE1 TYR 103 0.15 0.2375
889 CG TYR 103 0.15 896 CE2 TYR 103 0.15 0.2377
969 CG TRP 112 0.15 975 CE2 TRP 112 0.15 0.2196
970 CD1 TRP 112 0.15 972 CD2 TRP 112 0.15 0.2191
970 CD1 TRP 112 0.15 975 CE2 TRP 112 0.15 0.2134
972 CD2 TRP 112 0.15 978 CZ2 TRP 112 0.15 0.2334
976 CE3 TRP 112 0.15 982 CH2 TRP 112 0.15 0.2334
1133 C SER 131 0.15 1137 CA THR 132 0.15 0.2385
1148 C ALA 133 0.15 1152 CA MET 134 0.15 0.2399
1210 CB ASN 140 0.15 1216 C ASN 140 0.15 0.2395
1228 CG TYR 142 0.15 1233 CE1 TYR 142 0.15 0.2358
1228 CG TYR 142 0.15 1235 CE2 TYR 142 0.15 0.2374
1231 CD2 TYR 142 0.15 1237 CZ TYR 142 0.15 0.2397
1240 C TYR 142 0.15 1244 CA ALA 143 0.15 0.2358
1297 CB VAL 149 0.15 1300 C VAL 149 0.15 0.239
1414 CG1 ILE 164 0.15 1415 CG2 ILE 164 0.15 0.2399
1428 CG TYR 166 0.15 1433 CE1 TYR 166 0.15 0.2337
1431 CD2 TYR 166 0.15 1437 CZ TYR 166 0.15 0.2367
1443 CA PRO 167 0.15 1445 CG PRO 167 0.15 0.2364
1473 CD1 TYR 170 0.15 1481 CZ TYR 170 0.15 0.2358
1475 CD2 TYR 170 0.15 1481 CZ TYR 170 0.15 0.2349
1506 CB VAL 173 0.15 1509 C VAL 173 0.15 0.2383
1635 CG PHE 188 0.15 1640 CE1 PHE 188 0.15 0.2374
1635 CG PHE 188 0.15 1642 CE2 PHE 188 0.15 0.2383
1636 CD1 PHE 188 0.15 1644 CZ PHE 188 0.15 0.2397
1638 CD2 PHE 188 0.15 1644 CZ PHE 188 0.15 0.2385
1737 CB PRO 200 0.15 1739 CD PRO 200 0.15 0.2391
1760 CA VAL 204 0.15 1763 CG2 VAL 204 0.15 0.2367
1770 CG TYR 205 0.15 1775 CE1 TYR 205 0.15 0.2387
1770 CG TYR 205 0.15 1777 CE2 TYR 205 0.15 0.2375
1806 CD1 TYR 208 0.15 1808 CD2 TYR 208 0.15 0.2378
1808 CD2 TYR 208 0.15 1814 CZ TYR 208 0.15 0.2371
1820 CA PRO 209 0.15 1823 CD PRO 209 0.15 0.2371
1858 CB TYR 213 0.15 1860 CD1 TYR 213 0.15 0.2399
1859 CG TYR 213 0.15 1864 CE1 TYR 213 0.15 0.2334
1859 CG TYR 213 0.15 1866 CE2 TYR 213 0.15 0.2349
1864 CE1 TYR 213 0.15 1866 CE2 TYR 213 0.15 0.238
1895 C LEU 216 0.15 1899 CA ASN 217 0.15 0.2391
1964 CG HISA 225 0.15 1968 CE1 HISA 225 0.15 0.2109
1967 CD2 HISA 225 0.15 1968 CE1 HISA 225 0.15 0.2122
1970 C HISA 225 0.15 1974 CA VAL 226 0.15 0.2388
2048 CG LYSH 236 0.15 2050 CE LYSH 236 0.15 0.2377
2061 CG HISB 237 0.15 2064 CE1 HISB 237 0.15 0.2181
2063 CD2 HISB 237 0.15 2064 CE1 HISB 237 0.15 0.2159
2070 CA PRO 238 0.15 2072 CG PRO 238 0.15 0.2335
2188 CD1 LEU 249 0.15 2189 CD2 LEU 249 0.15 0.2392
2236 CG TYR 255 0.15 2241 CE1 TYR 255 0.15 0.24
2237 CD1 TYR 255 0.15 2239 CD2 TYR 255 0.15 0.2369
2239 CD2 TYR 255 0.15 2245 CZ TYR 255 0.15 0.2361
2284 CG PHE 260 0.15 2289 CE1 PHE 260 0.15 0.239
2284 CG PHE 260 0.15 2291 CE2 PHE 260 0.15 0.2389
2289 CE1 PHE 260 0.15 2291 CE2 PHE 260 0.15 0.239
2302 CD1 TYR 261 0.15 2304 CD2 TYR 261 0.15 0.2383
2302 CD1 TYR 261 0.15 2310 CZ TYR 261 0.15 0.2396
2306 CE1 TYR 261 0.15 2308 CE2 TYR 261 0.15 0.2397
2319 CG TYR 262 0.15 2324 CE1 TYR 262 0.15 0.2384
2322 CD2 TYR 262 0.15 2328 CZ TYR 262 0.15 0.2381
2331 C TYR 262 0.15 2335 CA GLY 263 0.15 0.2379
Atoms outside box ( 10.4505 10.4505 10.4505 ):
(These may occur often and are normally not a problem)
atom# name residue r_vdw coordinate
2433 OW SOL 274 0.105 -0.027 5.42 3.13
2435 HW2 SOL 274 0.04 -0.028 5.49 3.2
2436 OW SOL 275 0.105 -0.026 8.55 3.55
2438 HW2 SOL 275 0.04 -0.035 8.46 3.49
2439 OW SOL 276 0.105 -0.025 10.3 1.25
2442 OW SOL 277 0.105 -0.025 9.44 8.7
2443 HW1 SOL 277 0.04 -0.035 9.39 8.78
2445 OW SOL 278 0.105 -0.023 7.68 8.41
2448 OW SOL 279 0.105 -0.022 0.399 1.09
2450 HW2 SOL 279 0.04 -0.037 0.341 1.17
(maybe more)
gcq#253: "(That makes 100 errors; please try again.)" (TeX)
==============================================================
I decide to run the gmxcheck with the xtc trajectory after the deshuffle with
all the others files and I have the following output:
-bash-2.05b$ gmxcheck -f 1scnMD_MV_imp.xtc -c 1scn_MD_TPR.tpr -e
1scn_MD_ENER.edr >output2
Option Filename Type Description
------------------------------------------------------------
-f 1scnMD_MV_imp.xtc Input, Opt! Generic trajectory: xtc trr trj gro g96
pdb
-f2 traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb
-s1 top1.tpr Input, Opt. Generic run input: tpr tpb tpa xml
-s2 top2.tpr Input, Opt. Generic run input: tpr tpb tpa xml
-c 1scn_MD_TPR.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96
pdb xml
-e 1scn_MD_ENER.edr Input, Opt! Generic energy: edr ene
-e2 ener2.edr Input, Opt. Generic energy: edr ene
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 0 Set the nicelevel
-vdwfac real 0.8 Fraction of sum of VdW radii used as warning
cutoff
-bonlo real 0.4 Min. fract. of sum of VdW radii for bonded atoms
-bonhi real 0.7 Max. fract. of sum of VdW radii for bonded atoms
-tol real 0 Relative tolerance for comparing real values
defined as 2*(a-b)/(|a|+|b|)
-lastener string Last energy term to compare (if not given all are
tested). It makes sense to go up until the
Pressure.
Reading frame 0 time 0.000
# Atoms 2857
Precision 0.001 (nm)
Last frame 12218 time 12218.001
Item #frames Timestep (ps)
Step 12219 1
Time 12219 1
Lambda 0
Coords 12219 1
Velocities 0
Forces 0
Box 12219 1
Checking energy file 1scn_MD_ENER.edr
Opened 1scn_MD_ENER.edr as single precision energy file
frame: 0 (index 0), t: 0.000
Reading frame 12210 time 12210.001
Last frame read 12217
WARNING: Incomplete frame: nr 12218 time 12217.001
Found 12217 frames with a timestep of 1 ps.
Checking coordinate file 1scn_MD_TPR.tpr
Reading file 1scn_MD_TPR.tpr, VERSION 3.2.1 (single precision)
Reading file 1scn_MD_TPR.tpr, VERSION 3.2.1 (single precision)
110722 atoms in file
coordinates found
box found
velocities found
Kinetic energy: 411498 (kJ/mol)
Assuming the number of degrees of freedom to be Natoms * 3 or Natoms * 2,
the velocities correspond to a temperature of the system
of 297.993 K or 446.99 K respectively.
Checking for atoms closer than 0.8 and not between 0.4 and 0.7,
relative to sum of Van der Waals distance:
Opening library file /usr/local/gromacs/share/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/top/atommass.dat
Opening library file /usr/local/gromacs/share/top/vdwradii.dat
Opening library file /usr/local/gromacs/share/top/dgsolv.dat
atom# name residue r_vdw atom# name residue r_vdw distance
39 CA PRO 5 0.15 41 CG PRO 5 0.15 0.2354
50 CD1 TYR 6 0.15 52 CD2 TYR 6 0.15 0.2392
54 CE1 TYR 6 0.15 56 CE2 TYR 6 0.15 0.2398
72 CG1 ILE 8 0.15 73 CG2 ILE 8 0.15 0.2366
78 CA PRO 9 0.15 80 CG PRO 9 0.15 0.236
191 CD1 PHE 21 0.15 193 CD2 PHE 21 0.15 0.2399
191 CD1 PHE 21 0.15 199 CZ PHE 21 0.15 0.2372
193 CD2 PHE 21 0.15 199 CZ PHE 21 0.15 0.2378
242 CG1 VAL 26 0.15 243 CG2 VAL 26 0.15 0.2307
263 CG1 VAL 28 0.15 264 CG2 VAL 28 0.15 0.2362
352 CG HISB 39 0.15 355 CE1 HISB 39 0.15 0.2161
354 CD2 HISB 39 0.15 355 CE1 HISB 39 0.15 0.2176
381 CD1 LEU 42 0.15 382 CD2 LEU 42 0.15 0.2381
415 C GLY 46 0.15 419 CA GLY 47 0.15 0.2385
441 CD1 PHE 50 0.15 443 CD2 PHE 50 0.15 0.2366
441 CD1 PHE 50 0.15 449 CZ PHE 50 0.15 0.2359
443 CD2 PHE 50 0.15 449 CZ PHE 50 0.15 0.2365
493 CD1 TYR 56 0.15 495 CD2 TYR 56 0.15 0.235
497 CE1 TYR 56 0.15 499 CE2 TYR 56 0.15 0.2387
560 CG HISA 63 0.15 564 CE1 HISA 63 0.15 0.2189
563 CD2 HISA 63 0.15 564 CE1 HISA 63 0.15 0.2187
586 CG HISB 66 0.15 589 CE1 HISB 66 0.15 0.2114
588 CD2 HISB 66 0.15 589 CE1 HISB 66 0.15 0.215
732 CB PRO 85 0.15 734 CD PRO 85 0.15 0.233
774 CG TYR 90 0.15 781 CE2 TYR 90 0.15 0.2377
775 CD1 TYR 90 0.15 783 CZ TYR 90 0.15 0.2344
777 CD2 TYR 90 0.15 783 CZ TYR 90 0.15 0.2392
846 CB SER 97 0.15 849 C SER 97 0.15 0.2389
889 CG TYR 103 0.15 894 CE1 TYR 103 0.15 0.2375
889 CG TYR 103 0.15 896 CE2 TYR 103 0.15 0.2377
969 CG TRP 112 0.15 975 CE2 TRP 112 0.15 0.2196
970 CD1 TRP 112 0.15 972 CD2 TRP 112 0.15 0.2191
970 CD1 TRP 112 0.15 975 CE2 TRP 112 0.15 0.2134
972 CD2 TRP 112 0.15 978 CZ2 TRP 112 0.15 0.2334
976 CE3 TRP 112 0.15 982 CH2 TRP 112 0.15 0.2334
1133 C SER 131 0.15 1137 CA THR 132 0.15 0.2385
1148 C ALA 133 0.15 1152 CA MET 134 0.15 0.2399
1210 CB ASN 140 0.15 1216 C ASN 140 0.15 0.2395
1228 CG TYR 142 0.15 1233 CE1 TYR 142 0.15 0.2358
1228 CG TYR 142 0.15 1235 CE2 TYR 142 0.15 0.2374
1231 CD2 TYR 142 0.15 1237 CZ TYR 142 0.15 0.2397
1240 C TYR 142 0.15 1244 CA ALA 143 0.15 0.2358
1297 CB VAL 149 0.15 1300 C VAL 149 0.15 0.239
1414 CG1 ILE 164 0.15 1415 CG2 ILE 164 0.15 0.2399
1428 CG TYR 166 0.15 1433 CE1 TYR 166 0.15 0.2337
1431 CD2 TYR 166 0.15 1437 CZ TYR 166 0.15 0.2367
1443 CA PRO 167 0.15 1445 CG PRO 167 0.15 0.2364
1473 CD1 TYR 170 0.15 1481 CZ TYR 170 0.15 0.2358
1475 CD2 TYR 170 0.15 1481 CZ TYR 170 0.15 0.2349
1506 CB VAL 173 0.15 1509 C VAL 173 0.15 0.2383
1635 CG PHE 188 0.15 1640 CE1 PHE 188 0.15 0.2374
1635 CG PHE 188 0.15 1642 CE2 PHE 188 0.15 0.2383
1636 CD1 PHE 188 0.15 1644 CZ PHE 188 0.15 0.2397
1638 CD2 PHE 188 0.15 1644 CZ PHE 188 0.15 0.2385
1737 CB PRO 200 0.15 1739 CD PRO 200 0.15 0.2391
1760 CA VAL 204 0.15 1763 CG2 VAL 204 0.15 0.2367
1770 CG TYR 205 0.15 1775 CE1 TYR 205 0.15 0.2387
1770 CG TYR 205 0.15 1777 CE2 TYR 205 0.15 0.2375
1806 CD1 TYR 208 0.15 1808 CD2 TYR 208 0.15 0.2378
1808 CD2 TYR 208 0.15 1814 CZ TYR 208 0.15 0.2371
1820 CA PRO 209 0.15 1823 CD PRO 209 0.15 0.2371
1858 CB TYR 213 0.15 1860 CD1 TYR 213 0.15 0.2399
1859 CG TYR 213 0.15 1864 CE1 TYR 213 0.15 0.2334
1859 CG TYR 213 0.15 1866 CE2 TYR 213 0.15 0.2349
1864 CE1 TYR 213 0.15 1866 CE2 TYR 213 0.15 0.238
1895 C LEU 216 0.15 1899 CA ASN 217 0.15 0.2391
1964 CG HISA 225 0.15 1968 CE1 HISA 225 0.15 0.2109
1967 CD2 HISA 225 0.15 1968 CE1 HISA 225 0.15 0.2122
1970 C HISA 225 0.15 1974 CA VAL 226 0.15 0.2388
2048 CG LYSH 236 0.15 2050 CE LYSH 236 0.15 0.2377
2061 CG HISB 237 0.15 2064 CE1 HISB 237 0.15 0.2181
2063 CD2 HISB 237 0.15 2064 CE1 HISB 237 0.15 0.2159
2070 CA PRO 238 0.15 2072 CG PRO 238 0.15 0.2335
2188 CD1 LEU 249 0.15 2189 CD2 LEU 249 0.15 0.2392
2236 CG TYR 255 0.15 2241 CE1 TYR 255 0.15 0.24
2237 CD1 TYR 255 0.15 2239 CD2 TYR 255 0.15 0.2369
2239 CD2 TYR 255 0.15 2245 CZ TYR 255 0.15 0.2361
2284 CG PHE 260 0.15 2289 CE1 PHE 260 0.15 0.239
2284 CG PHE 260 0.15 2291 CE2 PHE 260 0.15 0.2389
2289 CE1 PHE 260 0.15 2291 CE2 PHE 260 0.15 0.239
2302 CD1 TYR 261 0.15 2304 CD2 TYR 261 0.15 0.2383
2302 CD1 TYR 261 0.15 2310 CZ TYR 261 0.15 0.2396
2306 CE1 TYR 261 0.15 2308 CE2 TYR 261 0.15 0.2397
2319 CG TYR 262 0.15 2324 CE1 TYR 262 0.15 0.2384
2322 CD2 TYR 262 0.15 2328 CZ TYR 262 0.15 0.2381
2331 C TYR 262 0.15 2335 CA GLY 263 0.15 0.2379
Atoms outside box ( 10.4505 10.4505 10.4505 ):
(These may occur often and are normally not a problem)
atom# name residue r_vdw coordinate
2433 OW SOL 274 0.105 -0.027 5.42 3.13
2435 HW2 SOL 274 0.04 -0.028 5.49 3.2
2436 OW SOL 275 0.105 -0.026 8.55 3.55
2438 HW2 SOL 275 0.04 -0.035 8.46 3.49
2439 OW SOL 276 0.105 -0.025 10.3 1.25
2442 OW SOL 277 0.105 -0.025 9.44 8.7
2443 HW1 SOL 277 0.04 -0.035 9.39 8.78
2445 OW SOL 278 0.105 -0.023 7.68 8.41
2448 OW SOL 279 0.105 -0.022 0.399 1.09
2450 HW2 SOL 279 0.04 -0.037 0.341 1.17
(maybe more)
gcq#286: "Lets Kill the Fucking Band" ( Tom Savini - From Dusk til Dawn )
===============================================================
As could be seen this way the program see the correct time from the
trajectory. This could be due to the deshuffle??? What could cause this???
Best regards
Anthony
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