[gmx-users] g_energy= Different Average values?
Hi I have read through the manual but could not get it. Would you please explain it more? Thank you Lin Chih-Ying Lin wrote: Hi After the command, g_energy -f abc.edr -o abc.xvg the average values is printed out on the screen. Energy Average RMSDFluct. Drift Tot-Drift Potential -267323 375.096 374.647 -0.12711-63.5543 Kinetic En. 51901.5 259.034 259.015 -0.02151-10.7574 Total Energy -215421 275.52 274.683 -0.14862 -74.3106 Temperature 302.825 1.51136 1.51125 -0.00013 -0.06277 Pressure (bar) 0.963727133.498 133.335 0.04560222.8012 Volume 221.643 0.3626250.3624248.36E-050.041823 Density (SI)990.272 1.62111 1.6202 -0.00038 -0.18852 but the average values are different than calculation from the instantaneous data in the abc.xvg I sum up all the instantaneous data in the abc.xvg and average them. I got different average data as those shown up on the screen after g_energy command. The average values reported in the .edr file are not necessarily the averages of the values in the .edr file. See manual appendix. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] .mdp = Dihedral Angles conflict Bond Constraints ?
Hi Lin, lincs-warnangle = 30 this allows each covalent bond to rotate at most 30 degrees This line says to issue a warning when a bond rotates more than 30 degrees. It doesn't say lincs-maxangle or something along those lines, indicating prohibiting such rotations. Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] using editconf to duplicate membrane
Hi Bing, You do want to use genconf for that (the way you use it, editconf scales the coordinates). genconf -f xxx.pdb -nbox 2 2 1 -o zzz.pdb The thing to make sure is that all molecules are whole before processing them with genconf. The other possibility is to use editconf to translate a few copies of your system and then stitch these fiels together. But genconf is quicker and more convenient. Cheers, Tsjerk On Tue, Jul 7, 2009 at 7:26 AM, Bing Bingjarbin...@gmail.com wrote: Dear all, I want to extend the membrane into 512 POPC with the starting structure of 128 POPC. I 've used :- editconf -f xxx.pdb -scale 2 2 1 -o zzz.pdb. I noticed that the pdb file that generated by editconf have only 1 set of 128 popc. Using vmd, the extended structure is in pieces, the no bond between each atom. When i checked the pdb file, i didn't find any atomic coordination for the extended set of POPC. Did i missed out anything here? or what I've done is wrong here? When i used genconf , the extended structure looks fine. But, i found some discussion regarding genconf whereby the structure will not be in one pieces if this command is used. Please advice. Thank in advance. Regards, bing ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Where are the source codes?
Hi I have installed the Gromacs and I want to see the source codes. Which directory can I find them? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about template.c?
Hi
inside template.c =
#include statutil.h
#include typedefs.h
#include smalloc.h
#include vec.h
#include copyrite.h
#include statutil.h
#include tpxio.h
what are they?
and, where are they?
thank you
Lin
/*
* $Id: template.c,v 1.4 2001/07/23 15:28:29 lindahl Exp $
*
*This source code is part of
*
* G R O M A C S
*
* GROningen MAchine for Chemical Simulations
*
*VERSION 3.0
*
* Copyright (c) 1991-2001
* BIOSON Research Institute, Dept. of Biophysical Chemistry
* 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.
*
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README COPYING
* files - if they are missing, get the official version at www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
*
* Do check out http://www.gromacs.org , or mail us at grom...@gromacs.org .
*
* And Hey:
* Gyas ROwers Mature At Cryogenic Speed
*/
/* This line is only for CVS version info */
static char *SRCID_template_c = $Id: template.c,v 1.4 2001/07/23 15:28:29 linda
hl Exp $;
#include statutil.h
#include typedefs.h
#include smalloc.h
#include vec.h
#include copyrite.h
#include statutil.h
#include tpxio.h
int main(int argc,char *argv[])
{
static char *desc[] = {
this is a small test program meant to serve as a template ,
when writing your own analysis tools. The advantage of ,
using gromacs for this is that you have access to all ,
information in the topology, and your program will be ,
able to handle all types of coordinates and trajectory ,
files supported by gromacs. Go ahead and try it! ,
This test version just writes the coordinates of an ,
arbitrary atom to standard out for each frame. You can ,
select which atom you want to examine with the -n argument.
};
static int n=1;
/* Extra arguments - but note how you always get the begin/end
* options when running the program, without mentioning them here!
*/
t_pargs pa[] = {
{ -n, FALSE, etINT, {n},
Plot data for atom number n (starting on 1)
}
};
t_topology top;
char title[STRLEN];
t_trxframe fr;
rvec *xtop;
matrix box;
intstatus;
intflags = TRX_READ_X;
t_filenm fnm[] = {
{ efTPS, NULL, NULL, ffREAD }, /* this is for the topology */
{ efTRX, -f, NULL, ffREAD } /* and this for the trajectory */
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
/* This is the routine responsible for adding default options,
* calling the X/motif interface, etc. */
parse_common_args(argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
/* We don't need any topology information to write the coordinates,
* but to show how it works we start by writing the name and
* charge of the selected atom. It returns a boolean telling us
* whether the topology was found and could be read
*/
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,top,xtop,NULL,box,TRUE);
sfree(xtop);
n=n-1; /* Our enumeration started on 1, but C starts from 0 */
/* check that this atom exists */
if(n0 || n(top.atoms.nr))
{
printf(Error: Atom number %d is out of range.\n,n);
exit(1);
}
printf(Atom name: %s\n,*(top.atoms.atomname[n]));
printf(Atom charge: %f\n,top.atoms.atom[n].q);
/* The first time we read data is a little special */
read_first_frame(status,ftp2fn(efTRX,NFILE,fnm),fr,flags);
/* This is the main loop over frames */
do {
/* coordinates are available in the vector fr.x
* you can find this and all other structures in
* the types directory under the gromacs include dir.
* Note how flags determines wheter to read x/v/f!
*/
printf(Coordinates at t=%8.3f : %8.5f %8.5f %8.5f\n,fr.time,fr.x[n][XX],fr
.x[n][YY],fr.x[n][ZZ]);
} while(read_next_frame(status,fr));
thanx(stderr);
return 0;
}
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[gmx-users] xdr library. Just for an example.
Hi, Can anybody share any working code which uses xdr-1.1 library? - Just to consult. Thank you very much in advance, Vitaly ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] xdr library. Just for an example.
Hi Vitali, There should be such code with then library itself. Ran. Vitaly V. Chaban wrote: Hi, Can anybody share any working code which uses xdr-1.1 library? - Just to consult. Thank you very much in advance, Vitaly ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Where are the source codes?
On Jul 7, 2009, at 9:28 AM, Chih-Ying Lin wrote: Hi I have installed the Gromacs and I want to see the source codes. Which directory can I find them? gromacs-4.0.5/src gromacs-4.0.5/include Carsten ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] about template.c?
On Jul 7, 2009, at 9:35 AM, Chih-Ying Lin wrote: Hi inside template.c = #include statutil.h #include typedefs.h #include smalloc.h #include vec.h #include copyrite.h #include statutil.h #include tpxio.h what are they? and, where are they? Go to the gromacs-4.0.5 directory and find out with find . -name 'statutil.h' where e.g. statutil.h resides. Carsten ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] False C6/C12 parameter for DMSO and chloroform in GROMOS 45a3 force field (ffG45a3)
Hi Roman, checking the mentioned original publication on GROMOS96 finally convinced me that you're right. It even says: If another combination rule ... is to be used to obtain C6ij and C12ij or if these mixed atom type pair parameters are not related to the single atom type van der Waals parameters ..., the interaction parameters for the pair of atom types ij must be explicitly given ...In the GROMOS force field this is the case for the van der Waals parameters for the solvents chloroform and DMSO. The origin of the DMSO parameters in ffG43a1 can be found in Liu et al. A Force Field for Liquid Dimethyl Sulfoxide and Physical Properties of Liquid Dimethyl Sulfoxide Calculated Using Molecular Dynamics Simulations J. Am. Chem. Soc. 1995, 117, 4363-4366. In this publication they actually use different combination rules as I already assumed in my previous mail. Cheers, Markus Roman Affentranger schrieb: Hi Markus I can not quite follow your arguments. The original publication on the GROMOS96 43a1 force field (W.F. van Gunsteren et al., Biomolecular Simulation: The GROMOS96 manual and user guide, Hochschulverlag AG an der ETH Zürich, 1996, Zürich, Switzerland) explicitly gives the pair parameters for interactions between non-equal atom types of DMSO (and of chloroform). See table 2.5.6.2.6 of the mentioned book. ffG43a1nb.itp actually contains these values. ffG45a3nb.itp contains the pair parameter one would obtain from the atomic parameters using eq. 5.3 in the GROMACS 4.0 manual. So the question is not so much which one is the right combination rule, since the pair parameter are given explicitly in the original reference of the GROMOS96 43a1 force field, and the values of DMSO (and chloroform) have not been reparametrized for the 45a3 force field. Cheers, Roman On Mon, Jul 6, 2009 at 5:07 PM, Markus Tusch mtu...@mail.upb.de wrote: Roman Affentranger schrieb: Dear gmx-users (and developers ;-) I believe there are false LJ pair-parameters in gromacs' implementation of the GROMOS 45a3 force field for interactions between the atoms of DMSO, and between the atoms of chloroform. The C6/C12 pair paramteters for CDMSO-SDMSO, ODMSO-SDMSO, ODMSO-CDMSO, and CLCHL-CCHL, HCHL-CCHL, HCHL-CLCHL in ffG45a3nb.itp are simply the (root of the) product of the individual atomic parameters, whereas separate parameters - with no relation to the atomic ones - are defined in the original GROMOS force field. Hi Roman, I think there actually is a relation of the pair parameters to the individual atomic parameters in G43a1 as well as in G45a3 since all of the values are based on the same epsilon and sigma numbers. (For DMSO: epsilon = 1.297 kJ/mol for S, 1.7154 for O, 0.9414 for CH3 sigma = 0.356 nm for S, 0.263 for O, 0.366 for CH3) The difference in the C6/C12 pair parameters apparently is due to the use of different combination rules (see GROMACSmanual-4.0.pdf, chapter 5.3.3). For G45a3 equations (5.1) and (5.3) are used to calculate the respective pair parameters, whereas for G43a1 eq. (5.4) and after that (5.1) are used. So I guess the question is, which is the right way for the combination? Cheers, Markus The errors are there in the force field files distributed with gromacs version 4.0.5 all the way down to at least version 3.2.1 (it's as far as I've looked), and also in the ffG45a3.tar.gz file to be found at http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Force_fields For example: The lines in ffG45a3nb.itp read: CDMSOSDMSO 1 0.009777435 2.1627421e-05 ... ODMSOSDMSO 1 0.004897196 4.0192831e-06 ODMSOCDMSO 1 0.0045335636 4.0434685e-06 However, they should be CDMSOSDMSO 1 0.0097827 2.16523e-05 ... ODMSOSDMSO 1 0.0052442 4.6094e-06 ODMSOCDMSO 1 0.0049187 4.7597e-06 as they are in the GROMOS 43a1 force field. A similar problem holds for chloroform (atoms CCHL, CLCHL and HCHL). Find attached a corrected version of ffG45a3nb.itp. Cheers, Roman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] bonds rotating more than 30 and segmentation fault.
Dear users, I am trying to simulate a non protein molecule and have included the necessary parameters in the ff*.rtp file. I first encountered an error in the grompp step, so i modified my .mdp files such that the rlist, rvdw and rcoulomb values are set to 0.5. Now, while carrying out the mdrun for the position restraint step, I am getting a segmentation fault and a LINCS warning for the dihedrals that exceed 30. I do not know how to proceed and I'm using version 3.3.3 so the bug in the earlier version should have been fixed. I have also tried other suggestions in the forum with no effect. Here is my pr.mdp file title = cpeptide position restraining warnings= 10 cpp = /lib/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 1; total 20.0 ps. nstcomm = 1 nstxout = 10 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 rlist = 0.5 coulombtype = PME rcoulomb= 0.5 rvdw= 0.5 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.10.1 tc-grps= Proteinother ref_t = 300300 ; Pressure coupling is not on Pcoupl = no 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 and this is the error I am encountering. Back Off! I just backed up md.log to ./#md.log.2# Reading file NOR_pr.tpr, VERSION 3.3.3 (single precision) Back Off! I just backed up ener.edr to ./#ener.edr.2# starting mdrun 'Protein in water' 1 steps, 20.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 361281.968750 (between atoms 2 and 7) rms 231973.328125 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 2 89.70.1530 43840.2148 0.1530 1 5 89.80.1530 44279.3516 0.1530 2 3 89.30.1530 51527.6133 0.1530 2 7 89.10.1530 55276.2969 0.1530 3 4 89.50.1530 22948.2949 0.1530 3 6 88.50.1530 20192.1895 0.1530 4 5 88.80.1530 8407.1387 0.1530 4 7 89.30.1530 26344.8340 0.1530 5 6 91.30.1530 33359.8477 0.1530 6 7 88.60.1530 13846.0684 0.1530 Segmentation fault I have been trying to solve this problem for quite some time now. It would be very helpful if you can suggest some way to work around this problem. regards Rukmani Sridharan ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] about template.c?
On Tue, 2009-07-07 at 00:35 -0700, Chih-Ying Lin wrote: Hi inside template.c = #include statutil.h #include typedefs.h #include smalloc.h #include vec.h #include copyrite.h #include statutil.h #include tpxio.h what are they? and, where are they? Those are GROMACS headers, to compile you need to add -I /path/to/gromacs/include -I /path/to/gromacs/include/types to the C compiler flags. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bonds rotating more than 30 and segmentation fault.
you may want to have a look at the cutoff used by the force field you defined your molecule in! 0.5 is definitely too small. did you minimized? if your starting configuration does not correspond to the topology, the use of position restrains (-DPOSRES) if you actually define them will be a problem ... I am trying to simulate a non protein molecule and have included the necessary parameters in the ff*.rtp file. I first encountered an error in the grompp step, so i modified my .mdp files such that the rlist, rvdw and rcoulomb values are set to 0.5. Now, while carrying out the mdrun for the position restraint step, I am getting a segmentation fault and a LINCS warning for the dihedrals that exceed 30. I do not know how to proceed and I'm using version 3.3.3 so the bug in the earlier version should have been fixed. I have also tried other suggestions in the forum with no effect. Here is my pr.mdp file title = cpeptide position restraining warnings= 10 cpp = /lib/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 1; total 20.0 ps. nstcomm = 1 nstxout = 10 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 rlist = 0.5 coulombtype = PME rcoulomb= 0.5 rvdw= 0.5 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.10.1 tc-grps= Proteinother ref_t = 300300 ; Pressure coupling is not on Pcoupl = no 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 and this is the error I am encountering. Back Off! I just backed up md.log to ./#md.log.2# Reading file NOR_pr.tpr, VERSION 3.3.3 (single precision) Back Off! I just backed up ener.edr to ./#ener.edr.2# starting mdrun 'Protein in water' 1 steps, 20.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 361281.968750 (between atoms 2 and 7) rms 231973.328125 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 2 89.70.1530 43840.2148 0.1530 1 5 89.80.1530 44279.3516 0.1530 2 3 89.30.1530 51527.6133 0.1530 2 7 89.10.1530 55276.2969 0.1530 3 4 89.50.1530 22948.2949 0.1530 3 6 88.50.1530 20192.1895 0.1530 4 5 88.80.1530 8407.1387 0.1530 4 7 89.30.1530 26344.8340 0.1530 5 6 91.30.1530 33359.8477 0.1530 6 7 88.60.1530 13846.0684 0.1530 Segmentation fault I have been trying to solve this problem for quite some time now. It would be very helpful if you can suggest some way to work around this problem. regards Rukmani Sridharan ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: g_energy= Different Average values?
Chih-Ying Lin wrote: Hi I have read through the manual but could not get it. Would you please explain it more? Normally the energy file does not store the value at every step. So the average over all the steps will differ from the average over the stored steps. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_energy= Different Average values from the screen than calculation of .xvg?
Hi After the command, g_energy -f abc.edr -o abc.xvg the average values is printed out on the screen. EnergyAverage RMSDFluct. Drift Tot-Drift Potential -267323 375.096 374.647 -0.12711 -63.5543 Kinetic En. 51901.5 259.034 259.015 -0.02151-10.7574 Total Energy -215421 275.52 274.683 -0.14862-74.3106 Temperature 302.825 1.51136 1.51125 -0.00013-0.06277 Pressure (bar) 0.963727133.498 133.335 0.04560222.8012 Volume 221.643 0.3626250.3624248.36E-05 0.041823 Density (SI)990.272 1.62111 1.6202 -0.00038-0.18852 but the average values are different than calculation from the instantaneous data in the abc.xvg I sum up all the instantaneous data in the abc.xvg and average them. I got different average data as those shown up on the screen after g_energy command. How do the Gromacs get the average values, which shows up on the screen directly after the command g_energy? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] -xy option for g_rdf
Dear GMX-users, I'm using g_rdf -xy for pure water box (about 1000 waters), but it just stopped after selecting two index groups (simply waters). Have you had the same experience with g_rdf -xy?Is it a bug? but, I couldn't find that in the Bugzilla. Any comments will be very appreciated. Thanks, best, Hwankyu. _ 강력해진 보안성, 아웃룩을 닮아 편리해진 기능들로 무장한 Windows Live Hotmail! 지금 로그인해 보세요! http://www.hotmail.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] using GROMACS in SDS-water simulations
Dear gmx-users, I have a general question: to your knowledge, is there anybody that has used GROMACS previously to simulate a protein in a mixture of SDS+water (not in a micelle or in a layer of SDS)? I searched for papers or publications, but I didn't found anything relevant to my topic. Thanks for help and best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabo...@isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm If you think you are too small to make a difference, try sleeping with a mosquito ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Why is triclinic geometry not retained in confout.gro?
Hello gmx-users I?m having problems with my mdrun (probably a newbie question). I?m using the latest version of gromacs. I have my .pdb file (or .gro), mdp and .top files ready and can generate the .tpr file. When I run this (with an simple energy minimisation) the simulation runs to completion (I?ve only tried a very short run) but I get a strange confout.gro file as output. My unit cell is triclinic and my input files (both .pdb or .gro) looks fine in VMD. The confgro.out file is strange in that the box has been converted to cubic when I view it in VMD. Is this normal? Why doesn?t it retain the triclinic shape I defined in the pdb file? I?ve been over the topology but my inexperienced eyes can?t see anything wrong. One thing I did notice is that when I looked at the tpr file, all of my atom numbers were shifted by 1 with regards to my topology file i.e In the tpr file, the first angle listed is for atoms 364, 0 and 413 Angle: nr: 9492 iatoms: 0 type=11 (ANGLES) 364 0 413 But in the topology file the first angle I have listed is for 365, 1 and 414. [ angles ] ; ai aj ak funct c0 c1 365 1 414 1 109.04 289.095916 In my pdb and top file my atoms are labelled from 1-1071 whereas in the .tpr file they are labelled from 0-1070. Is this something I should be worried about? Below I have pasted sections of my top file, my pdb file and my .mdp file. I?d appreciate if someone could look over and see that my triclinic unit cell is correctly defined (although the input file looks OK when viewed in VMD). If anyone has the time or inclination to try and run my files (if that helps spot the error), I would be happy to e-mail them and would be very grateful, If you see anything else that looks odd, please feel free to point it out as I am new to gromacs, Thanks in advance, Jenny pdb CRYST1 46.421 43.630 18.960 90.00 90.00 120.00 P 1 1 ATOM 1 SI X 1 -22.104 -1.646 -1.173 1.00 0.00 SI ATOM 2 SI X 1 8.325 -18.877 8.329 1.00 0.00 SI ATOM 3 SI X 1 27.146 -12.854 3.831 1.00 0.00 SI ATOM 4 SI X 1 -14.415 -11.322 4.375 1.00 0.00 SI ATOM 5 SI X 1 -10.624 -15.731 -7.960 1.00 0.00 SI ... ATOM289 O X 1 19.588 -18.099 7.519 1.00 0.00 ATOM290 O X 1 -19.450 0.838 -2.667 1.00 0.00 ... ATOM794 O X 1 22.966 -15.478 -8.908 1.00 0.00 ATOM795 O X 1 17.234 -5.878 -2.785 1.00 0.00 ATOM796 OH X 1 -7.634 -18.464 -3.746 1.00 0.00 ATOM797 H X 1 -7.655 -18.213 -4.662 1.00 0.00 H ATOM798 OH X 1 7.669 -17.509 7.819 1.00 0.00 ATOM799 H X 1 8.061 -17.122 7.046 1.00 0.00 H ATOM 1068 OH X 1 4.808 -14.731 1.210 1.00 0.00 ATOM 1069 H X 1 3.887 -14.515 1.123 1.00 0.00 H ATOM 1070 OH X 1 18.839 0.763 -8.266 1.00 0.00 ATOM 1071 H X 1 18.283 0.835 -9.032 1.00 0.00 H END Topology file [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 no 1.01.0 ; ; [ atomtypes ] ; typemasschargeptype c6c12 SI 28.08 1.28 A0.000 0.00 O 15.999-0.64 A0.27081.538176 OH 15.999-0.53 A0.30 1.538176 H 1.008 0.21 A0.000 0.000 ; [ moleculetype ] ; Namenrexcl MCM 3 [ atoms ] ; nr typeresnr residue atomcgnrcharge mass 1 SI 1 MCM SI 1 1.2804993 28.086 2 SI 1 MCM SI 2 1.2804993 28.086 3 SI 1 MCM SI 3 1.2804993 28.086 4 SI 1 MCM SI 4 1.2804993 28.086 5 SI 1 MCM SI 5 1.2804993 28.086 ... 289 O 1 MCM O 289 -0.64024965 15.9994 290 O 1 MCM O 290 -0.64024965 15.9994 ... 794 O 1 MCM O 794 -0.64024965 15.9994 795 O 1 MCM O 795 -0.64024965 15.9994 796 OH 1 MCM OH 796 -0.52612471 15.9994 797 H 1 MCM H 797 0.20599988 1.00797 798 OH 1 MCM OH 798 -0.52612471 15.9994 799 H 1 MCM H 799 0.20599988 1.00797 ... 1068
[gmx-users] Including K+ in gromos96
Date: Mon, 6 Jul 2009 16:52:51 -0500 From: sadhna joshi sadhna.jo...@gmail.com Subject: [gmx-users] including K ion in gromos96 To: gmx-users@gromacs.org Message-ID: ffc8f9170907061452y4b5ea1e4jacfc4b81dfc12...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 hi, I am using gromacs 3.3.1 and ions.itp does not have K ion (in gromos96). I tried to include it by making K.itp and including in topology file. I get the following error.. Invalid order for directive atoms, file K.itp, line 1 I am not sure where I am wrong,,, thanks sadhna Hi sadhna, You must read the manual chapter five, after, you must see the ions.itp and ?nb.itp files and note if there are parameters for K ion. You must include the parameters for the ion K and for the Cl ions, if you try to create a file k.itp, follow the same steps but adding the mass of the ion. Good Luck Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Why is triclinic geometry not retained in confout.gro?
Hi Jenny, Check chapter 3 of the manual regarding PBC. There is no box in PBC (a box defines PBC, but PBC does not define a box). The rectangular brick is just one of the ways to represent the unit cell. If you insist in seeing a triclinic unit cell, use trjconv -ur triclinic -pbc inbox. Cheers, Tsjerk On Tue, Jul 7, 2009 at 7:18 PM, Jennifer Williamsjennifer.willi...@ed.ac.uk wrote: Hello gmx-users I?m having problems with my mdrun (probably a newbie question). I?m using the latest version of gromacs. I have my .pdb file (or .gro), mdp and .top files ready and can generate the .tpr file. When I run this (with an simple energy minimisation) the simulation runs to completion (I?ve only tried a very short run) but I get a strange confout.gro file as output. My unit cell is triclinic and my input files (both .pdb or .gro) looks fine in VMD. The confgro.out file is strange in that the box has been converted to cubic when I view it in VMD. Is this normal? Why doesn?t it retain the triclinic shape I defined in the pdb file? I?ve been over the topology but my inexperienced eyes can?t see anything wrong. One thing I did notice is that when I looked at the tpr file, all of my atom numbers were shifted by 1 with regards to my topology file i.e In the tpr file, the first angle listed is for atoms 364, 0 and 413 Angle: nr: 9492 iatoms: 0 type=11 (ANGLES) 364 0 413 But in the topology file the first angle I have listed is for 365, 1 and 414. [ angles ] ; ai aj ak funct c0 c1 365 1 414 1 109.04 289.095916 In my pdb and top file my atoms are labelled from 1-1071 whereas in the .tpr file they are labelled from 0-1070. Is this something I should be worried about? Below I have pasted sections of my top file, my pdb file and my .mdp file. I?d appreciate if someone could look over and see that my triclinic unit cell is correctly defined (although the input file looks OK when viewed in VMD). If anyone has the time or inclination to try and run my files (if that helps spot the error), I would be happy to e-mail them and would be very grateful, If you see anything else that looks odd, please feel free to point it out as I am new to gromacs, Thanks in advance, Jenny pdb CRYST1 46.421 43.630 18.960 90.00 90.00 120.00 P 1 1 ATOM 1 SI X 1 -22.104 -1.646 -1.173 1.00 0.00 SI ATOM 2 SI X 1 8.325 -18.877 8.329 1.00 0.00 SI ATOM 3 SI X 1 27.146 -12.854 3.831 1.00 0.00 SI ATOM 4 SI X 1 -14.415 -11.322 4.375 1.00 0.00 SI ATOM 5 SI X 1 -10.624 -15.731 -7.960 1.00 0.00 SI ... ATOM 289 O X 1 19.588 -18.099 7.519 1.00 0.00 ATOM 290 O X 1 -19.450 0.838 -2.667 1.00 0.00 ... ATOM 794 O X 1 22.966 -15.478 -8.908 1.00 0.00 ATOM 795 O X 1 17.234 -5.878 -2.785 1.00 0.00 ATOM 796 OH X 1 -7.634 -18.464 -3.746 1.00 0.00 ATOM 797 H X 1 -7.655 -18.213 -4.662 1.00 0.00 H ATOM 798 OH X 1 7.669 -17.509 7.819 1.00 0.00 ATOM 799 H X 1 8.061 -17.122 7.046 1.00 0.00 H ATOM 1068 OH X 1 4.808 -14.731 1.210 1.00 0.00 ATOM 1069 H X 1 3.887 -14.515 1.123 1.00 0.00 H ATOM 1070 OH X 1 18.839 0.763 -8.266 1.00 0.00 ATOM 1071 H X 1 18.283 0.835 -9.032 1.00 0.00 H END Topology file [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 no 1.0 1.0 ; ; [ atomtypes ] ; type mass charge ptype c6 c12 SI 28.08 1.28 A 0.000 0.00 O 15.999 -0.64 A 0.2708 1.538176 OH 15.999 -0.53 A 0.30 1.538176 H 1.008 0.21 A 0.000 0.000 ; [ moleculetype ] ; Name nrexcl MCM 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 SI 1 MCM SI 1 1.2804993 28.086 2 SI 1 MCM SI 2 1.2804993 28.086 3 SI 1 MCM SI 3 1.2804993 28.086 4 SI 1 MCM SI 4 1.2804993 28.086 5 SI 1 MCM SI 5 1.2804993 28.086 ... 289 O 1 MCM O 289 -0.64024965 15.9994 290 O 1 MCM O 290 -0.64024965 15.9994 ... 794 O 1 MCM O 794 -0.64024965 15.9994 795 O 1 MCM O 795 -0.64024965 15.9994 796 OH 1 MCM
Re: [gmx-users] Installation problem:fftw3f lib. not found.
hI, I apologize for late reply. The script you mentioned worked completely fine. I guess I was using different shell. Thanks a lot On Wed, Jul 1, 2009 at 2:11 PM, Florian Dommert domm...@icp.uni-stuttgart.de wrote: * Shobhit Kudesia shobhit.kude...@gmail.com [2009-06-30 21:19:47 -0400]: Hi, I installed fftw as follows (creating single- and double-precision versions) : ./configure --enable-threads --enable-float --prefix=/home/kudesias/fftw make make install make distclean ./configure --enable-threads --prefix=/home/kudesias/fftw make make install I also used export CPPFLAGS=-I/home/kudesias/fftw/include export LDFLAGS=-L/home/kudesias/fftw/lib ( Initially I used I in place of L so I corrected it) On using the configure script ./configure --enable-mpi I get the following error then checking how to hardcode library paths into programs... immediate checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... 1 checking for sqrt in -lm... yes checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). I will be glad if you can help with this. I tried your procedure on my computer and the configure script finished without trouble. Are your sure using fftw**3** ? In case you use fftw2 you have to tell the script. Another problem can be that you set the enviroment variables in another shell window as you execute the configure script, because then CPPFLAGS and LDFLAGS are not present anymore. To be on the safe side put all in one line: ./configure --prefix=$HOME/gmx4 LDFLAGS=-L$HOME/fftw/lib CPPFLAGS=-I$HOME/fftw/include This command line should work for you, in case FFTW3 is located as you mentioned before. So try copypaste and tell us over the mailing list what happend. Flo Thanks On Thu, Jun 25, 2009 at 2:08 AM, Florian Dommert domm...@icp.uni-stuttgart.de wrote: * Shobhit Kudesia shobhit.kude...@gmail.com [2009-06-25 01:55:00 +0530]: Hi , During the ./configure of gromacs on my Bash Shell, I get the following error: configure: error: Cannot find fftw3f library I have installed fftw3 files in a directory other than usr/local. I have installed fftw3 both with double and single precision but I still get the error while configuration of GROMACS for default single precision. I have also included the libraries usinG CPPFLAGS LDFLAGS. If you have installed the single version of FFTW3 and supply the corresponding CPPFLAGS and LDFLAGS to configure then the script will find the libraries. So two errors are very likely though we do not anything about your installation: * a small typo in the configure line ( if you present it here, everybody can judge this ) * the installation of the single precision fftw3f failed for any reasons Flo Any help will be appreciated ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert !! PGP-ENCODED emails preferred !! ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- With Warm Regards Shobhit Kudesia 3rd year Undergraduate Department of Biotechnology IIT Kharagpur ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home:
[gmx-users] analysis eror
Hi gromacs users. I need help with the old data generated by gromacs. It is about a year older. I used the command and the output is: s...@linux-g1cj:~/Desktop/283 g_energy -f md283.edr -o 283te.xvg :-) G R O M A C S (-: Good gRace! Old Maple Actually Chews Slate :-) VERSION 3.0.5 (-: Copyright (c) 1991-2001, 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. :-) g_energy (-: Option Filename Type Description -f md283.edr Input Generic energy: edr ene -f2 ener.edr Input, Opt. Generic energy: edr ene -s topol.tpr Input, Opt. Generic run input: tpr tpb tpa -o 283te.xvg Output xvgr/xmgr file -viol violaver.xvg Output, Opt. xvgr/xmgr file -pairs pairs.xvg Output, Opt. xvgr/xmgr file -corr enecorr.xvg Output, Opt. xvgr/xmgr file -vis visco.xvg Output, Opt. xvgr/xmgr file -ravg runavgdf.xvg Output, Opt. xvgr/xmgr 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 -[no]w bool no View output xvg, xpm, eps and pdb files -[no]fee bool no Do a free energy estimate -fetemp real 300 Reference temperature for free energy calculation -zero real 0 Subtract a zero-point energy -[no]sum bool no Sum the energy terms selected rather than display them all -[no]dp bool no Print energies in high precision -[no]mutot bool no Compute the total dipole moment from the components -skip int 0 Skip number of frames between data points -[no]aver bool no Print also the X1,t and sigma1,t, only if only 1 energy is requested -nmol int 1 Number of molecules in your sample: the energies are divided by this number -ndf int 3 Number of degrees of freedom per molecule. Necessary for calculating the heat capacity -[no]fluc bool no Calculate autocorrelation of energy fluctuations rather than energy itself -acflen int -1 Length of the ACF, default is half the number of frames -[no]normalize bool yes Normalize ACF -P enum 0 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 -fitfn enum none Fit function: none, exp, aexp, exp_exp or vac -ncskip int 0 Skip N points in the output file of correlation functions -beginfit real 0 Time where to begin the exponential fit of the correlation function -endfit real -1 Time where to end the exponential fit of the correlation function, -1 is till the end Opened md283.edr as single precision energy file Select the terms you want from the following list End your selection with 0 1= Angle 2= Proper Dih. 3=Ryckaert-Bell. 4= LJ-14 5= Coulomb-14 6= LJ (SR) 7= LJ (LR) 8= Coulomb (SR) 9= Coul. recip. 10=Position Rest. 11= Potential 12= Kinetic En. 13= Total Energy 14= Temperature 15=Pressure (bar) 16= Box-X 17= Box-Y 18= Box-Z 19= Volume 20= Density (SI) 21= pV 22= Vir-XX 23= Vir-XY 24= Vir-XZ 25= Vir-YX 26= Vir-YY 27= Vir-YZ 28= Vir-ZX 29= Vir-ZY 30= Vir-ZZ 31= Pres-XX (bar) 32= Pres-XY (bar) 33= Pres-XZ (bar) 34= Pres-YX (bar) 35= Pres-YY (bar) 36= Pres-YZ (bar) 37= Pres-ZX (bar) 38= Pres-ZY (bar) 39= Pres-ZZ (bar) 40= #Surf*SurfTen 41= Pcoupl-Mu-XX 42= Pcoupl-Mu-YY 43= Pcoupl-Mu-ZZ 44= Mu-X 45= Mu-Y 46= Mu-Z 47= T-Protein 48= T-Non-Protein 49= Lamb-Protein 50=Lamb-Non-Protein 13 0 Fatal error: Could not open 283te.xvg s...@linux-g1cj:~/Desktop/283 your help is necessary for my success. Regards LAL BADSHAH New Email names for you! Get the Email name you#39;ve always wanted on the new @ymail and @rocketmail. Hurry before someone else
[gmx-users] Fatal error
Hi gromacs users, the other fatal error which is produces from my last year data is: s...@linux-g1cj:~/Desktop/283 g_rms -s em.tpr -f md283.trr -o md283-rmsd.xvg :-) G R O M A C S (-: GROningen MAchine for Chemical Simulation :-) VERSION 3.0.5 (-: Copyright (c) 1991-2001, 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. :-) g_rms (-: Option Filename Type Description -s em.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -f md283.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 md283-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 -[no]fit bool yes Fit to reference structure -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 em.tpr, VERSION 3.3.1 (single precision) Fatal error: reading tpx file (em.tpr) version 40 with version 20 program So now whats the main problem with this data: Regards,LAL BADSHAH New Email addresses available on Yahoo! Get the Email name you#39;ve always wanted on the new @ymail and @rocketmail. Hurry before someone else does! http://mail.promotions.yahoo.com/newdomains/aa/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Fatal error
The error tells you what the problem is: Fatal error: reading tpx file (em.tpr) version 40 with version 20 program You are trying to read an em.tpr file that was generated using version 40 (as noted by the header it is GROMACS 3.3.1) using a version 20 program (as noted by the header it is GROMACS 3.0.5). You have to use a program that is at least 3.3.1 for it to work. Would be better if you were using the current 4.0.x version. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of s lal badshah Sent: Wednesday, 8 July 2009 8:17 AM To: gromacs Subject: [gmx-users] Fatal error Hi gromacs users, the other fatal error which is produces from my last year data is: s...@linux-g1cj:~/Desktop/283 g_rms -s em.tpr -f md283.trr -o md283-rmsd.xvg :-) G R O M A C S (-: GROningen MAchine for Chemical Simulation :-) VERSION 3.0.5 (-: Copyright (c) 1991-2001, 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. :-) g_rms (-: Option Filename Type Description -s em.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -f md283.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 md283-rmsd.xvg Outputxvgr/xmgr file -mirrmsdmir.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 -niceint 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 boolyes PBC check -[no]fit boolyes Fit to reference structure -prevint 0 Compare with previous frame -[no]split bool no Split graph where time is zero -skipint 1 Only write every nr-th frame to matrix -skip2int 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 -nlevelsint 80 Number of levels in the matrices Reading file em.tpr, VERSION 3.3.1 (single precision) Fatal error: reading tpx file (em.tpr) version 40 with version 20 program So now whats the main problem with this data: Regards, LAL BADSHAH Get your new Email address! http://sg.rd.yahoo.com/aa/mail/domainchoice/mail/signature/*http:/mail. promotions.yahoo.com/newdomains/aa/ Grab the Email name you've always wanted before someone else does! ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatal error
Hi Gromacs user, I changed the version and this time it gave the following error s...@linux-g1cj:~/Desktop/283 g_energy -f md283.edr -o md283-TE.xvg :-) G R O M A C S (-: Gnomes, ROck Monsters And Chili Sauce :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, 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_energy (-: Option Filename Type Description -f md283.edr Input Generic energy: edr ene -f2 ener.edr Input, Opt. Generic energy: edr ene -s topol.tpr Input, Opt. Generic run input: tpr tpb tpa xml -o md283-TE.xvg Output xvgr/xmgr file -viol violaver.xvg Output, Opt. xvgr/xmgr file -pairs pairs.xvg Output, Opt. xvgr/xmgr file -ora orienta.xvg Output, Opt. xvgr/xmgr file -ort orientt.xvg Output, Opt. xvgr/xmgr file -oda orideva.xvg Output, Opt. xvgr/xmgr file -odr oridevr.xvg Output, Opt. xvgr/xmgr file -odt oridevt.xvg Output, Opt. xvgr/xmgr file -oten oriten.xvg Output, Opt. xvgr/xmgr file -corr enecorr.xvg Output, Opt. xvgr/xmgr file -vis visco.xvg Output, Opt. xvgr/xmgr file -ravg runavgdf.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgr bool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -[no]fee bool no Do a free energy estimate -fetemp real 300 Reference temperature for free energy calculation -zero real 0 Subtract a zero-point energy -[no]sum bool no Sum the energy terms selected rather than display them all -[no]dp bool no Print energies in high precision -[no]mutot bool no Compute the total dipole moment from the components -skip int 0 Skip number of frames between data points -[no]aver bool no Print also the X1,t and sigma1,t, only if only 1 energy is requested -nmol int 1 Number of molecules in your sample: the energies are divided by this number -ndf int 3 Number of degrees of freedom per molecule. Necessary for calculating the heat capacity -[no]fluc bool no Calculate autocorrelation of energy fluctuations rather than energy itself -[no]orinst bool no Analyse instantaneous orientation data -[no]ovec bool no Also plot the eigenvectors with -oten -acflen int -1 Length of the ACF, default is half the number of frames -[no]normalize bool yes Normalize ACF -P enum 0 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 -fitfn enum none Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7 or exp9 -ncskip int 0 Skip N points in the output file of correlation functions -beginfit real 0 Time where to begin the exponential fit of the correlation function -endfit real -1 Time where to end the exponential fit of the correlation function, -1 is till the end Opened md283.edr as single precision energy file Select the terms you want from the following list - Angle Proper-Dih. Ryckaert-Bell. LJ-14 Coulomb-14 LJ-(SR) LJ-(LR) Coulomb-(SR) Coul.-recip. Position-Rest. Potential Kinetic-En. Total-Energy Temperature Pressure-(bar) Box-X Box-Y Box-Z Volume Density-(SI) pV Vir-XX Vir-XY Vir-XZ Vir-YX Vir-YY Vir-YZ Vir-ZX Vir-ZY
Re: [gmx-users] Installation problem:fftw3f lib. not found.
* Shobhit Kudesia shobhit.kude...@gmail.com [2009-07-08 02:53:22 +0530]: hI, I apologize for late reply. The script you mentioned worked completely fine. I guess I was using different shell. Thanks a lot You're welcome. Just one remark. When setting any CPPFLAGS or LDFLAGS it is often helpful to put this statements in the same command line before the call of ./configure. Though a properly generated configure script in the correct sense of autoconf, some other scripts seem to make trouble ( for example the MPlayer as I was told ) /Flo On Wed, Jul 1, 2009 at 2:11 PM, Florian Dommert domm...@icp.uni-stuttgart.de wrote: * Shobhit Kudesia shobhit.kude...@gmail.com [2009-06-30 21:19:47 -0400]: Hi, I installed fftw as follows (creating single- and double-precision versions) : ./configure --enable-threads --enable-float --prefix=/home/kudesias/fftw make make install make distclean ./configure --enable-threads --prefix=/home/kudesias/fftw make make install I also used export CPPFLAGS=-I/home/kudesias/fftw/include export LDFLAGS=-L/home/kudesias/fftw/lib ( Initially I used I in place of L so I corrected it) On using the configure script ./configure --enable-mpi I get the following error then checking how to hardcode library paths into programs... immediate checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... 1 checking for sqrt in -lm... yes checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). I will be glad if you can help with this. I tried your procedure on my computer and the configure script finished without trouble. Are your sure using fftw**3** ? In case you use fftw2 you have to tell the script. Another problem can be that you set the enviroment variables in another shell window as you execute the configure script, because then CPPFLAGS and LDFLAGS are not present anymore. To be on the safe side put all in one line: ./configure --prefix=$HOME/gmx4 LDFLAGS=-L$HOME/fftw/lib CPPFLAGS=-I$HOME/fftw/include This command line should work for you, in case FFTW3 is located as you mentioned before. So try copypaste and tell us over the mailing list what happend. Flo Thanks On Thu, Jun 25, 2009 at 2:08 AM, Florian Dommert domm...@icp.uni-stuttgart.de wrote: * Shobhit Kudesia shobhit.kude...@gmail.com [2009-06-25 01:55:00 +0530]: Hi , During the ./configure of gromacs on my Bash Shell, I get the following error: configure: error: Cannot find fftw3f library I have installed fftw3 files in a directory other than usr/local. I have installed fftw3 both with double and single precision but I still get the error while configuration of GROMACS for default single precision. I have also included the libraries usinG CPPFLAGS LDFLAGS. If you have installed the single version of FFTW3 and supply the corresponding CPPFLAGS and LDFLAGS to configure then the script will find the libraries. So two errors are very likely though we do not anything about your installation: * a small typo in the configure line ( if you present it here, everybody can judge this ) * the installation of the single precision fftw3f failed for any reasons Flo Any help will be appreciated ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert !! PGP-ENCODED emails preferred !! ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- With Warm Regards Shobhit Kudesia 3rd year Undergraduate Department of Biotechnology IIT Kharagpur ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't
[gmx-users] Convert trr into crd (amber format)
I came across a tool for making porcupine plots out of my PCA analysis, but first I need to perform the analysis with a program that accepts .cdr (amber traj) file format (the name of the program is PCAZIP). I would like to know if there is a way to convert my .trr trajectories into these .cdr ones. Or, in case you have a better solution for my problem, like a different analysis tool or something like that, it would also be very helpful. Thank you advance Fabrício Bracht ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Convert trr into crd (amber format)
Ragnarok sdf wrote: I came across a tool for making porcupine plots out of my PCA analysis, but first I need to perform the analysis with a program that accepts .cdr (amber traj) file format (the name of the program is PCAZIP). I would like to know if there is a way to convert my .trr trajectories into these .cdr ones. Or, in case you have a better solution for my problem, like a different analysis tool or something like that, it would also be very helpful. If disk space is not limiting, and high accuracy is not required, then using trjconv to convert to PDB and whatever tool AMBER has to convert to the .cdr format would work. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
