[gmx-users] Re: a flat plane boundary condition
Beckett W Sterner
bsterner at MIT.EDU
Wed May 25 21:56:56 CEST 2005
Hi,
Thats looks great for fixing one end of the protein, but I also want to
ensure that the rest of it is restricted to only half of space (the
impenetrable plane boundary condition). Or maybe I'm missing your
meaning. The constraint is important because as the protein exits the
pore it should begin to fold but it shouldn't clump around the residue
with fixed position.
Thanks,
Beckett
> You can freeze atoms in one, two or three dimensions. Check mdp options
> on www.gromacs.org
> On Wed, 2005-05-25 at 12:30 -0400, Beckett W Sterner wrote:
> > Hi,
> > I'm interested in doing a simple simulation of how a protein folds as it
> > slowly emerges from a pore through a cell membrane. I unfortunately do
> > not have a crystal structure for the pore, and would like to keep
> > computational costs to a minimum, so I'm interested in running an MD
> > simulation on the protein where one end is fixed to a flat plane with a 2d
> > periodic boundary condition. Is there a way to implement this in GROMACS,
> > perhaps using a force field?
> You can freeze atoms in one, two or three dimensions. Check mdp options
> on www.gromacs.org
> >
> > Thanks,
> > Beckett
> > _______________________________________________
> > 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.
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 25 May 2005 13:55:46 -0400
> From: Anthony Cruz <acb15885 at uprm.edu>
> Subject: Re: [gmx-users] g_rms Fatal error: Error: Too many iterations
> in routine JACOBI
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <200505251355.46962.acb15885 at uprm.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I do the gmxcheck and this is the result:
>
> Checking file 1scn_bx_w_fullMD_mv.trr
> trn version: GMX_trn_file (single precision)
> Reading frame 0 time 0.000
> # Atoms 110719
> Last frame 10500 time 10500.001
>
>
> Item #frames Timestep (ps)
> Step 10501 1
> Time 10501 1
> Lambda 10501 1
> Coords 10501 1
> Velocities 10501 1
> Forces 0
> Box 10501 1
> Checking coordinate file 1scn_bx_w_CL_TPR4fullMD.tpr
> Reading file 1scn_bx_w_CL_TPR4fullMD.tpr, VERSION 3.2.1 (single precision)
> Reading file 1scn_bx_w_CL_TPR4fullMD.tpr, VERSION 3.2.1 (single precision)
> 110719 atoms in file
> coordinates found
> box found
> velocities found
>
> Kinetic energy: 411492 (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 297.996 K or 446.995 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:
> WARNING: masses will be determined based on residue and atom names,
> this can deviate from the real mass of the atom type
> In case you use free energy of solvation predictions:
>
> ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
> D. Eisenberg and A. D. McLachlan
> Solvation energy in protein folding and binding
> Nature 319 (1986) pp. 199-203
> -------- -------- --- Thank You --- -------- --------
>
> 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
> #Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
> atom# name residue r_vdw atom# name residue r_vdw distance
> 40 CB PRO 5 0.15 42 CD PRO 5 0.15 0.2332
> 50 CD1 TYR 6 0.15 58 CZ TYR 6 0.15 0.2369
> 52 CD2 TYR 6 0.15 58 CZ TYR 6 0.15 0.2358
> 78 CA PRO 9 0.15 80 CG PRO 9 0.15 0.2383
> 87 CB LEU 10 0.15 91 C LEU 10 0.15 0.2399
> 149 C VAL 16 0.15 153 CA GLN 17 0.15 0.2398
> 190 CG PHE 21 0.15 195 CE1 PHE 21 0.15 0.2395
> 191 CD1 PHE 21 0.15 193 CD2 PHE 21 0.15 0.2393
> 193 CD2 PHE 21 0.15 199 CZ PHE 21 0.15 0.2369
> 244 C VAL 26 0.15 248 CA LYSH 27 0.15 0.2371
> 277 CG1 VAL 30 0.15 278 CG2 VAL 30 0.15 0.2398
> 302 CB THR 33 0.15 306 C THR 33 0.15 0.2383
> 352 CG HISB 39 0.15 355 CE1 HISB 39 0.15 0.2174
> 354 CD2 HISB 39 0.15 355 CE1 HISB 39 0.15 0.2169
> 361 CA PRO 40 0.15 364 CD PRO 40 0.15 0.2395
> 362 CB PRO 40 0.15 364 CD PRO 40 0.15 0.2387
> 383 C LEU 42 0.15 387 CA ASN 43 0.15 0.2391
> 440 CG PHE 50 0.15 447 CE2 PHE 50 0.15 0.2371
> 441 CD1 PHE 50 0.15 449 CZ PHE 50 0.15 0.2331
> 443 CD2 PHE 50 0.15 449 CZ PHE 50 0.15 0.2371
> 459 C VAL 51 0.15 463 CA ALA 52 0.15 0.2376
> 492 CG TYR 56 0.15 497 CE1 TYR 56 0.15 0.2334
> 492 CG TYR 56 0.15 499 CE2 TYR 56 0.15 0.2398
> 497 CE1 TYR 56 0.15 499 CE2 TYR 56 0.15 0.2375
> 558 CA HISA 63 0.15 560 CG HISA 63 0.15 0.2398
> 560 CG HISA 63 0.15 564 CE1 HISA 63 0.15 0.212
> 563 CD2 HISA 63 0.15 564 CE1 HISA 63 0.15 0.2126
> 586 CG HISB 66 0.15 589 CE1 HISB 66 0.15 0.2163
> 588 CD2 HISB 66 0.15 589 CE1 HISB 66 0.15 0.2109
> 692 C GLY 79 0.15 696 CA VAL 80 0.15 0.2391
> 698 CG1 VAL 80 0.15 699 CG2 VAL 80 0.15 0.2384
> 732 CB PRO 85 0.15 734 CD PRO 85 0.15 0.2341
> 751 C VAL 87 0.15 755 CA SER 88 0.15 0.2397
> 775 CD1 TYR 90 0.15 783 CZ TYR 90 0.15 0.2391
> 777 CD2 TYR 90 0.15 783 CZ TYR 90 0.15 0.2398
> 817 CA VAL 94 0.15 819 CG1 VAL 94 0.15 0.2397
> 890 CD1 TYR 103 0.15 892 CD2 TYR 103 0.15 0.2384
> 894 CE1 TYR 103 0.15 896 CE2 TYR 103 0.15 0.2346
> 929 CG1 VAL 107 0.15 930 CG2 VAL 107 0.15 0.2398
> 969 CG TRP 112 0.15 975 CE2 TRP 112 0.15 0.2231
> 970 CD1 TRP 112 0.15 972 CD2 TRP 112 0.15 0.2171
> 970 CD1 TRP 112 0.15 975 CE2 TRP 112 0.15 0.2157
> 975 CE2 TRP 112 0.15 976 CE3 TRP 112 0.15 0.2367
> 978 CZ2 TRP 112 0.15 980 CZ3 TRP 112 0.15 0.2378
> 1079 C MET 123 0.15 1083 CA SER 124 0.15 0.2396
> 1094 CD1 LEU 125 0.15 1095 CD2 LEU 125 0.15 0.239
> 1216 C ASN 140 0.15 1220 CA ALA 141 0.15 0.2389
> 1228 CG TYR 142 0.15 1233 CE1 TYR 142 0.15 0.2379
> 1229 CD1 TYR 142 0.15 1231 CD2 TYR 142 0.15 0.2377
> 1233 CE1 TYR 142 0.15 1235 CE2 TYR 142 0.15 0.2356
> 1251 CB ARG 144 0.15 1263 C ARG 144 0.15 0.2347
> 1347 C GLY 156 0.15 1351 CA ASN 157 0.15 0.2398
> 1428 CG TYR 166 0.15 1433 CE1 TYR 166 0.15 0.238
> 1428 CG TYR 166 0.15 1435 CE2 TYR 166 0.15 0.2363
> 1443 CA PRO 167 0.15 1446 CD PRO 167 0.15 0.2391
> 1473 CD1 TYR 170 0.15 1475 CD2 TYR 170 0.15 0.237
> 1473 CD1 TYR 170 0.15 1481 CZ TYR 170 0.15 0.2383
> 1477 CE1 TYR 170 0.15 1479 CE2 TYR 170 0.15 0.2392
> 1530 CG1 VAL 176 0.15 1531 CG2 VAL 176 0.15 0.2373
> 1635 CG PHE 188 0.15 1640 CE1 PHE 188 0.15 0.2336
> 1635 CG PHE 188 0.15 1642 CE2 PHE 188 0.15 0.2393
> 1640 CE1 PHE 188 0.15 1642 CE2 PHE 188 0.15 0.2399
> 1686 CB GLU 194 0.15 1691 C GLU 194 0.15 0.2396
> 1698 CD1 LEU 195 0.15 1699 CD2 LEU 195 0.15 0.2293
> 1736 CA PRO 200 0.15 1738 CG PRO 200 0.15 0.2346
> 1762 CG1 VAL 204 0.15 1763 CG2 VAL 204 0.15 0.2344
> 1771 CD1 TYR 205 0.15 1773 CD2 TYR 205 0.15 0.2366
> 1775 CE1 TYR 205 0.15 1777 CE2 TYR 205 0.15 0.2391
> 1806 CD1 TYR 208 0.15 1808 CD2 TYR 208 0.15 0.2383
> 1810 CE1 TYR 208 0.15 1812 CE2 TYR 208 0.15 0.2356
> 1859 CG TYR 213 0.15 1864 CE1 TYR 213 0.15 0.2375
> 1860 CD1 TYR 213 0.15 1862 CD2 TYR 213 0.15 0.24
> 1862 CD2 TYR 213 0.15 1868 CZ TYR 213 0.15 0.2396
> 1864 CE1 TYR 213 0.15 1866 CE2 TYR 213 0.15 0.2366
> 1954 CA PRO 224 0.15 1957 CD PRO 224 0.15 0.2351
> 1964 CG HISA 225 0.15 1968 CE1 HISA 225 0.15 0.2137
> 1967 CD2 HISA 225 0.15 1968 CE1 HISA 225 0.15 0.2127
> 2012 CB LEU 232 0.15 2014 CD1 LEU 232 0.15 0.2396
> 2032 CD1 LEU 234 0.15 2033 CD2 LEU 234 0.15 0.2395
> 2063 CD2 HISB 237 0.15 2064 CE1 HISB 237 0.15 0.2173
> 2070 CA PRO 238 0.15 2072 CG PRO 238 0.15 0.2387
> 2236 CG TYR 255 0.15 2243 CE2 TYR 255 0.15 0.2388
> 2241 CE1 TYR 255 0.15 2243 CE2 TYR 255 0.15 0.237
> 2284 CG PHE 260 0.15 2289 CE1 PHE 260 0.15 0.2363
> 2285 CD1 PHE 260 0.15 2287 CD2 PHE 260 0.15 0.2389
> 2287 CD2 PHE 260 0.15 2293 CZ PHE 260 0.15 0.2339
> 2301 CG TYR 261 0.15 2308 CE2 TYR 261 0.15 0.2389
> 2302 CD1 TYR 261 0.15 2310 CZ TYR 261 0.15 0.2358
> 2304 CD2 TYR 261 0.15 2310 CZ TYR 261 0.15 0.2395
> 2319 CG TYR 262 0.15 2326 CE2 TYR 262 0.15 0.2376
> 2324 CE1 TYR 262 0.15 2326 CE2 TYR 262 0.15 0.238
>
> Atoms outside box ( 10.4513 10.4513 10.4513 ):
> (These may occur often and are normally not a problem)
> atom# name residue r_vdw coordinate
> 2488 OW SOL 293 0.105 -0.034 2.79 4.15
> 2491 OW SOL 294 0.105 -0.031 5.54 9.37
> 2494 OW SOL 295 0.105 -0.024 3.92 10.1
> 2497 OW SOL 296 0.105 -0.02 5.24 10.3
> 2500 OW SOL 297 0.105 -0.018 4.16 8.09
> 2501 HW1 SOL 297 0.04 -0.027 4.18 8.19
> 2503 OW SOL 298 0.105 -0.018 6.61 5.17
> 2506 OW SOL 299 0.105 -0.016 1.37 7.5
> 2509 OW SOL 300 0.105 -0.015 2.23 9.93
> 2511 HW2 SOL 300 0.04 -0.048 2.29 10
> (maybe more)-bash-2.05b$ g_rms -f 1scn_bx_w_fullMD_mv.trr -s
> 1scn_bx_w_CL_TPR4fullMD.tpr -o
> :-) 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.
>
> :-) g_rms (-:
>
> Option Filename Type Description
> ------------------------------------------------------------
> -s 1scn_bx_w_CL_TPR4fullMD.tpr Input Structure+mass(db): tpr tpb
> tpa gro g96 pdb xml
> -f 1scn_bx_w_fullMD_mv.trr Input Generic trajectory: xtc trr trj
> gro g96 pdb
> -f2 traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb
> -n index.ndx Input, Opt. Index file
> -o rmsd.xvg Output xvgr/xmgr file
> -mir rmsdmir.xvg Output, Opt. xvgr/xmgr file
> -a avgrp.xvg Output, Opt. xvgr/xmgr file
> -dist rmsd-dist.xvg Output, Opt. xvgr/xmgr file
> -m rmsd.xpm Output, Opt. X PixMap compatible matrix file
> -bin rmsd.dat Output, Opt. Generic data file
> -bm bond.xpm Output, Opt. X PixMap compatible matrix file
>
> 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
> -b time -1 First frame (ps) to read from trajectory
> -e time -1 Last frame (ps) to read from trajectory
> -dt time -1 Only use frame when t MOD dt = first time (ps)
> -tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h
> -[no]w bool no View output xvg, xpm, eps and pdb files
> -what enum rmsd Structural difference measure: rmsd, rho or rhosc
> -[no]pbc bool yes PBC check
> -fit enum rot+trans Fit to reference structure: rot+trans,
> translation or none
> -prev int 0 Compare with previous frame
> -[no]split bool no Split graph where time is zero
> -skip int 1 Only write every nr-th frame to matrix
> -skip2 int 1 Only write every nr-th frame to matrix
> -max real -1 Maximum level in comparison matrix
> -min real -1 Minimum level in comparison matrix
> -bmax real -1 Maximum level in bond angle matrix
> -bmin real -1 Minimum level in bond angle matrix
> -nlevels int 80 Number of levels in the matrices
>
> Reading file 1scn_bx_w_CL_TPR4fullMD.tpr, VERSION 3.2.1 (single precision)
> Reading file 1scn_bx_w_CL_TPR4fullMD.tpr, VERSION 3.2.1 (single precision)
> Select group for least squares fit
> Opening library file /usr/local/gromacs/share/top/aminoacids.dat
> Group 0 ( System) has 110719 elements
> Group 1 ( Protein) has 2433 elements
> Group 2 ( Protein-H) has 1920 elements
> Group 3 ( C-alpha) has 274 elements
> Group 4 ( Backbone) has 822 elements
> Group 5 ( MainChain) has 1097 elements
> Group 6 (MainChain+Cb) has 1336 elements
> Group 7 ( MainChain+H) has 1364 elements
> Group 8 ( SideChain) has 1069 elements
> Group 9 ( SideChain-H) has 823 elements
> Group 10 ( Prot-Masses) has 2433 elements
> Group 11 ( Non-Protein) has 108286 elements
> Group 12 ( CL) has 4 elements
> Group 13 ( HOH) has 423 elements
> Group 14 ( SOL) has 107856 elements
> Group 15 ( CA) has 2 elements
> Group 16 ( NA) has 1 elements
> Group 17 ( Other) has 108286 elements
> Select a group: 1
> Selected 1: 'Protein'
> How many groups do you want to compare ? 1
> OK. I will compare 1 group
> Select group for RMSD calculation
> Opening library file /usr/local/gromacs/share/top/aminoacids.dat
> Group 0 ( System) has 110719 elements
> Group 1 ( Protein) has 2433 elements
> Group 2 ( Protein-H) has 1920 elements
> Group 3 ( C-alpha) has 274 elements
> Group 4 ( Backbone) has 822 elements
> Group 5 ( MainChain) has 1097 elements
> Group 6 (MainChain+Cb) has 1336 elements
> Group 7 ( MainChain+H) has 1364 elements
> Group 8 ( SideChain) has 1069 elements
> Group 9 ( SideChain-H) has 823 elements
> Group 10 ( Prot-Masses) has 2433 elements
> Group 11 ( Non-Protein) has 108286 elements
> Group 12 ( CL) has 4 elements
> Group 13 ( HOH) has 423 elements
> Group 14 ( SOL) has 107856 elements
> Group 15 ( CA) has 2 elements
> Group 16 ( NA) has 1 elements
> Group 17 ( Other) has 108286 elements
> Select a group: 1
> Selected 1: 'Protein'
> trn version: GMX_trn_file (single precision)
> Reading frame 0 time 0.000 Fatal error: Error: Too many iterations
> in routine JACOBI
>
> How I could resolve the problem???
>
> then I try g_rms:
>
>
> On Friday 20 May 2005 10:42 am, Anthony Cruz wrote:
> > How I could do that??? a new tpr??
> >
> > On Friday 20 May 2005 7:53 am, Xavier Periole wrote:
> > > Anthony Cruz wrote:
> > > >Hi:
> > > >I run a MD of a protein in water. when I try to analyse the trajectory
> > > > with g_rms the program stop by the following error :
> > > >Fatal error: Error: Too many iterations in routine JACOBI
> > > >What could be the cause? How I can resolve the problem???
> > >
> > > That is certainly due to a mismatch between your reference topology and
> > > the content of
> > > the trajectory ... make an topology that fits the trajectory.
> >
> > _______________________________________________
> > 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.
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 25 May 2005 13:48:43 -0500
> From: "Francesco Mercuri" <mercuri at email.com>
> Subject: [gmx-users] Time reversibility and settle
> To: gmx-users at gromacs.org
> Message-ID: <20050525184843.B8250101D9 at ws1-3.us4.outblaze.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> > > Hello and thank you for your reply.
> > > However, my question about the time reversibility of a leap-frog integrator
> > > with settle (e.g. for TIP3P water molecules) was concerned with the
> > > actual implementation in Gromacs, rather than the analytical point
> > > of view. In other words, is this implementation of leap-frog +
> > > settle still time-reversible in the limit of infinite numerical
> > > accuracy?
> > > This question arises since I tried different numerical
> > > accuracies (single, double and quadruple precision numbers and
> > > operations; for the latter I had to rewrite large parts of the
> > > code...) with, in all cases, similar (and pretty large)
> > > deviations from the "forward" trajectory when reversing the time.
> > > On the other hand, just bypassing the "settle" subroutine
> > > (e.g. by commenting all the code related to the original
> > > implementation of settle by Miyamoto and Kollman), it works as
> > > expected: the algorithm is almost perfectly time-reversible
> > > and the only "noise" is due to numerical inaccuracies, with
> > > deviations comparable, in the three different cases (single,
> > > double, long double) to the accuracy of numbers.
> > > Thus, I'm trying to understand whether just resetting the position
> > > of atoms, as done in the current implementation of "settle",
> > > still leads to a time-reversible MD (in the limit of infinite
> > > machine accuracy).
> > > Any suggestion about that?
> >
> > In the limit is should be time-reversible, unless there is a bug in
> > the settle algorithm, which I consider very unlikely.
> > Have you tried to use shake or lincs (with high precision settings)?
> >
> > There could be some other issues, but when the unconstrained
> > dynamics is reversible you have probably taken care of these:
> > You should not use temperature and pressure coupling (the new
> > version will have reversible Nose-Hoover coupling).
> > When reversing you should take care to use the proper velocities,
> > as x(t), v(t-t/2dt) is stored you need to take the velocities from
> > the next step when reversing.
> >
> > Berk.
>
> Hi again and thanks for your suggestions.
> Still in the search of better time-reversibility properties, I'd like
> to ask a few more questions.
> If I understood correctly, the leap-frog + settle algorithm is implemented
> in Gromacs according to the following steps:
>
> v'(t+dt/2) = v(t-dt/2) + dt*f(t)/m ("uncorrected" velocities)
> r'(t+dt) = r(t) + dt*v'(t+dt/2) (unconstrained move)
> r(t+dt) = settle[r'(t+dt)] (reset of atomic position calling "csettle")
> v(t+dt/2) = [r(t+dt)-r(t)]/dt (corrected velocities)
>
> is that correct?
> In this case, is not very clear to me how is it possible to "reverse" it,
> e.g. restarting from a [r(t),v(t+dt/2)] configuration and inverting the
> sign of dt, since the settle procedure modifies the atomic position in a
> way that is, apparently, not "reversible".
> Is any modification of the velocities needed?
>
> Another question concerns the preparation of restart files containing
> configurations like the one cited above for time-reversing purposes,
> i.e. [r(t),v(t+dt/2)] (instead of the default [r(t),v(t-dt/2)] ).
> I tried the quick and dirty way by just running one more MD step,
> converting the .trr file in ascii format, manually editing the
> ascii file in order to get the [r(t),v(t+dt/2)] configuration,
> pasting into a .gro file and converting back the .gro file into
> a .trr file for restarting. However, even if I modified the routine
> pr_rvecs in txtdump.c in order to have more decimal digits in the
> ascii files, the accuracy seems to be limited to the order of
> 1.e-8, whereas I expected a better accuracy for double precision
> numbers. Is there any better way to do that? Which is the accuracy
> with which numbers are stored in the .trr file (with double
> precision compilation)?
> Thank you again and best regards,
>
> Francesco
>
> --
> ___________________________________________________________
> Sign-up for Ads Free at Mail.com
> http://promo.mail.com/adsfreejump.htm
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 25 May 2005 20:54:30 +0200
> From: "Jordi Camps" <jcamps at lsi.upc.edu>
> Subject: [gmx-users] Adding ions
> To: "'Discussion list for GROMACS users'" <gmx-users at gromacs.org>
> Message-ID: <200505251854.j4PIsNFw028595 at dagon.lsi.upc.edu>
> Content-Type: text/plain; charset="US-ASCII"
>
> Here I come with more problems :-(
>
> I have a protein file with 126 residues. I generated the topology from the
> .gro file with pdb2gmx. Then I configured the box with editconf. Then I
> added the solvent with genbox. At least I wanted to neutralize the system
> with genion, but it gave me this error:
> Fatal error: pbc_dx called before init_pbc
> This time I think that I followed all the standard steps. Do you know which
> could be the cause of this error?
>
> The command was:
> $ genion -s 1agi.water.top -o 1agi.ion.gro -nn 6
> And the last lines before the error are:
> Selected 12: 'SOL'
> Number of (3-atomic) solvent molecules: 7092
> Doing single force calculation...
> Replacing solvent molecule 1626 (atom 6216) with Cl
> Fatal error: pbc_dx called before init_pbc
>
> Thank you in advance,
>
> --
>
> Jordi Camps Puchades
>
> Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
> UPC-CIRI
> c/. Jordi Girona 1-3
> Modul C6-E201 Tel. : 934 011 650
> E-08034 Barcelona Fax : 934 017 014
> Catalunya (Spain) e-mail: jcamps at lsi.upc.edu
>
>
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
>
>
> End of gmx-users Digest, Vol 13, Issue 66
> *****************************************
>
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