Re: [gmx-users] how to obtain error bar for plotting?
On 28/12/2011 6:59 PM, leila karami wrote: Dear Mark thanks for your reply. I have a general questions: For what parameters I can use g_analyze -av average.xvg -errbar stddev -f *.xvg?// //*** What quantity do you wish to show with an error bar? I want to show output from g_dist with an error bar. That's not a quantity. You need to be able to say something like I want to show with an error bar twice the standard error of the average distance between the terminal alpha-carbon atoms over my five simulations. Once you can do that you can start to construct commands with g_dist and g_analyze to achieve it. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] how to obtain error bar for plotting?
Dear Mark I am studying interaction between protein and dna, especially hydrogen bonds. using g-dist, I obtained distance between donor atom of protein and acceptor atom of dna. in this case, can I use g_analyze for obtaining error bar or stddev? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] SPC density
Thank you very much for your advice... I have tried including dispcorr = enerpres in my mdp file and the density increased a bit in a timescale of 5 ns but it is still far from the value expected for pure water. These are the new results: Statistics over 251 steps [ 0. thru 5000. ps ], 3 data sets All averages are exact over 251 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 2982.675632.67534 2.70867e-05 0.135433 Volume 126.133 0.529594 0.529323 1.17324e-05 0.0586622 Density (SI)978.1144.106214.10412 -9.08266e-05 -0.454133 Heat Capacity Cv: 12.4733 J/mol K (factor = 8.06157e-05) Isothermal Compressibility: 5.40447e-05 /bar Adiabatic bulk modulus:18503.2 bar I guess I should get 1000 g/cm^3 Any other suggestion? On Tue, Dec 27, 2011 at 6:23 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2011-12-27 17:57, Theodora García wrote: Dear all I am starting some MD simulations aimed to calculate the volume of a solute in water as a function of the concentration. First I ran a simulation of a box with 4124 SPC water molecules (similar number of molecules that will be later used with my solute) for which I got the following results after ~7.5 ns: dispcorr = enerpres Statistics over 3762001 steps [ 0. thru 7524.0005 ps ], 3 data sets All averages are exact over 3762001 steps Energy Average RMSD Fluct. Drift Tot-Drift --**--** --- Temperature 298125.156125.156 1.9202e-05 0.144476 Volume 126.90853.291753.2917 5.61522e-06 0.0422489 Density (SI)972.142408.201408.201 -4.30887e-05 -0.324199 Heat Capacity Cv: 16.9588 J/mol K (factor = 0.176389) Isothermal Compressibility: 0.543909 /bar Adiabatic bulk modulus:1.83854 bar Why am I obtaining so low density? The density seems to be constant over that timescale. This is my mdp file: constraints = all-bonds integrator = md dt = 0.002 nsteps = 250 nstxout = 5000 nstvout = 5 nstenergy = 1000 nstxtcout = 5000 energygrps = SOL nstlist = 5 ns_type = grid rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 coulombtype = PME fourierspacing = 0.15 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes Tcoupl = nose-hoover tau_t = 0.1 tc-grps = SOL ref_t = 298 Pcoupl = Parrinello-Rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 pcoupltype = isotropic gen_vel = yes gen_temp= 298 gen_seed= -1 Thanks in advance for any help... -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] how to obtain error bar for plotting?
Dear Mark can I obtain error bar twice the standard error of the average distance between the donor atom of protein and acceptor atom of dna over 1 simulation? should I do several simulation. Is 1 simulation enough? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] trjconv -nojump
- Forwarded Message - From: mohammad agha mra...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, December 27, 2011 8:59 PM Subject: Re: [gmx-users] trjconv and g_clustsize Thank you very much from your reply. I found out that my problem is at step c (-pbc nojump) because I exercised ngmx after steps a and b by: ngmx -f cluster.gro -s cluster.tpr and I viewed 2 micelles the same of result of md.trr (or md.xtc). I studied http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions according to your advice and I think that I should Extract the first frame from the trajectory as reference for removing jumps and then Remove jumps according step c, but I have a problem about this! May I ask you to check my steps, please? 1- trjconv -f md.xtc -s md.tpr -o cluster.gro -e 60 -pbc cluster (and I selected 2 surfactants for clustering group and 0 system for outpup group) 2- grompp -f md.mdp -c cluster.gro -o cluster.tpr -n index.ndx Then I did: ngmx -f cluster.gro -s cluster.tpr and I viewed 2 micelles. 3- trjconv -f cluster.gro -s cluster.tpr -dump 0 -o clusterdump.gro (and I selected 0 system for output group) 4- grompp -f md.mdp -c clusterdump.gro -o cluster1.tpr -n index.ndx 5- trjconv -f cluster.gro -s cluster1.tpr -pbc nojump -o clusternojump.xtc Then I did: ngmx -f clusternojump.xtc -s cluster1.tpr and I had the same previous problem. May I ask you to help me, please? Best Regards Sara From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, December 26, 2011 4:20 PM Subject: Re: [gmx-users] trjconv and g_clustsize On 12/26/2011 7:53 PM, mohammad agha wrote: Dear Prof. I have several questions about trjconv, please help me. In my simulation is created 2 micelles. 1- When I do 3 steps of micelle clustering as follows: a- trjconv -f md.xtc -o a_cluster.gro-e 60 -pbc cluster b- grompp -f md.mdp -c a_cluster.gro -o a_cluster.tpr c- trjconv -f md.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump I view 2 micelles according to result of my simulation in VMD but in ngmx isn't view 2 micelles but just is view 1 micelle and reminder of monomers are collected in several groups in different places. So you don't have a single cluster of atoms... so as trjconv -h notes, using -pbc cluster isn't very useful when you don't have a cluster of atoms. All my advice of two days ago on this point still applies. Is it right if my criterion be view in VMD and is my micelle clustering correct? It's correct if it looks the way you want it to. 2- If I select surfactants for clustering group and system for output group in step (a) and I select system for output group in step (c), command g_clustsize doesn't work correct, consequently, I did under step and made a .xtc file only for surfactants: i- trjconv -f md.trr -o md-surfactant.xtc -n index.ndx Then I did steps a, b and c for md-surfactant.xtc and in all of steps I selected surfactants for clustering and output group. Next, I did g_clustsize and it answered me correct. May I know that my way is correct, please? 3- By upper way I have 2 micelles that I got index.ndx file for cluster with maximum size by g_clustsize (maxcluster.ndx). May I know how can I use from this for next calculation if I want consider only maximum cluster with all of system (water and ion) in calculations (for example rdf, gyration and etc)? Again I think you are not using the word cluster in the sense the GROMACS tools are. Each micelle could be a cluster of atoms, or the pair of micelles could be a cluster of micelles. How to use the tools will differ according to what you are trying to calculate on what kind of cluster. Anyway, the atom numbers do not change with the configuration of the atoms, so the same index file group identifies the surfactant atoms in each frame. To identify the *time* of the configuration with the largest diameter, something like g_mindist -max might serve. However you may need to resolve your PBC issue first. Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or
Re: [gmx-users] SPC density
Hi I just saw the article Temperature Dependence of TIP3P, SPC, and TIP4P Water from NPT Monte Carlo Simulations: Seeking Temperatures of Maximum Density published in Journal of Computational Chemistry, Vol. 19, No. 10, 1179]1186 (1998). It gives 0.985 for SPC at 25 C with different setup... perhaps 0.978 is not so bad? On Wed, Dec 28, 2011 at 9:34 AM, Theodora García theodoraaagar...@gmail.com wrote: Thank you very much for your advice... I have tried including dispcorr = enerpres in my mdp file and the density increased a bit in a timescale of 5 ns but it is still far from the value expected for pure water. These are the new results: Statistics over 251 steps [ 0. thru 5000. ps ], 3 data sets All averages are exact over 251 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 2982.675632.67534 2.70867e-05 0.135433 Volume 126.133 0.529594 0.529323 1.17324e-05 0.0586622 Density (SI)978.1144.106214.10412 -9.08266e-05 -0.454133 Heat Capacity Cv: 12.4733 J/mol K (factor = 8.06157e-05) Isothermal Compressibility: 5.40447e-05 /bar Adiabatic bulk modulus:18503.2 bar I guess I should get 1000 g/cm^3 Any other suggestion? On Tue, Dec 27, 2011 at 6:23 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-12-27 17:57, Theodora García wrote: Dear all I am starting some MD simulations aimed to calculate the volume of a solute in water as a function of the concentration. First I ran a simulation of a box with 4124 SPC water molecules (similar number of molecules that will be later used with my solute) for which I got the following results after ~7.5 ns: dispcorr = enerpres Statistics over 3762001 steps [ 0. thru 7524.0005 ps ], 3 data sets All averages are exact over 3762001 steps Energy Average RMSD Fluct. Drift Tot-Drift --**--** --- Temperature 298125.156125.156 1.9202e-05 0.144476 Volume 126.90853.291753.2917 5.61522e-06 0.0422489 Density (SI)972.142408.201408.201 -4.30887e-05 -0.324199 Heat Capacity Cv: 16.9588 J/mol K (factor = 0.176389) Isothermal Compressibility: 0.543909 /bar Adiabatic bulk modulus:1.83854 bar Why am I obtaining so low density? The density seems to be constant over that timescale. This is my mdp file: constraints = all-bonds integrator = md dt = 0.002 nsteps = 250 nstxout = 5000 nstvout = 5 nstenergy = 1000 nstxtcout = 5000 energygrps = SOL nstlist = 5 ns_type = grid rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 coulombtype = PME fourierspacing = 0.15 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes Tcoupl = nose-hoover tau_t = 0.1 tc-grps = SOL ref_t = 298 Pcoupl = Parrinello-Rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 pcoupltype = isotropic gen_vel = yes gen_temp= 298 gen_seed= -1 Thanks in advance for any help... -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] how to use the modified gromacs 4.5.5's temple
how to use gromacs 4.5.5's temple
Dear teacher,
i have already modify the code, and also make it.
Attached is my modified code good.
Dear teacher,
how to use gromacs 4.5.5's temple?
I expect that it is not meant to be functional. It's meant to be a
template from which you can write functional code without having to work
too hard on making it work like GROMACS tools work.
Mark
i make the temple successful! And when i run it (./template -f traj.xtc -s
water.tpr -cutoff 2),
the output like this:
Reading file water.tpr, VERSION 4.5.5 (single precision)
Reading file water.tpr, VERSION 4.5.5 (single precision)
Specify a reference selection:
(one selection per line, 'help' for help)
help
SELECTION HELP
This program supports selections in addition to traditional index files.
Please read the subtopic pages (available through help topic) for more
information. Explanation of command-line arguments for specifying selections
can be found under the cmdline subtopic, and general selection syntax is
described under syntax. Available keywords can be found under keywords,
and concrete examples under examples. Other subtopics give more details on
certain aspects. help all prints the help for all subtopics.
Available subtopics:
cmdline syntax positions arithmetic keywords evaluation limitations
examples
thanks!!
Regards,
Bodu
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303 ; +8613820062885
E-mail: 2008d...@gmail.com ; dubo2...@tju.edu.cn
/*
*
*This source code is part of
*
* G R O M A C S
*
* GROningen MAchine for Chemical Simulations
*
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2009, 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.
*
* 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.
*
* For more info, check our website at http://www.gromacs.org
*/
#include gromacs/copyrite.h
#include gromacs/filenm.h
#include gromacs/macros.h
#include gromacs/pbc.h
#include gromacs/smalloc.h
#include gromacs/statutil.h
#include gromacs/vec.h
#include gromacs/xvgr.h
#include gromacs/nbsearch.h
#include gromacs/trajana.h
#define ATOMS 1000
#define ATOMS 1000
#define BIN 1000
/*! \brief
* Template analysis data structure.
*/
typedef struct
{
gmx_ana_selection_t *refsel;
FILE*fp;
real*ave;
real*n;
gmx_ana_nbsearch_t *nb;
realdibond[ATOMS][ATOMS][BIN];
int nbin;
int natoms;
realcutoff;
} t_analysisdata;
/*! \brief
* Function that does the analysis for a single frame.
*
* It is called once for each frame.
*/
static int
analyze_frame(t_topology *top, t_trxframe *fr, t_pbc *pbc,
int nr, gmx_ana_selection_t *sel[], void *data)
{
t_analysisdata *d = (t_analysisdata *)data;
int g, i,j,bin,m;
realfrave,distance;
int rc;
d-natoms=fr-natoms;
/* Here, you can do whatever analysis your program requires for a frame. */
//===edit by bodu 2011-12-25
for (i=0;ifr-natoms;i++)
for (j=i+1;jfr-natoms;j++)
for (m=0;md-nbin;m++)
d-dibond[i][j][m]=0.0;
for (i=0;ifr-natoms;i++)
for (j=i+1;jfr-natoms;j++){
distance=sqrt((fr-x[i][0]-fr-x[j][0])*(fr-x[i][0]-fr-x[j][0])+(fr-x[i][1]-fr-x[j][1])*(fr-x[i][1]-fr-x[j][1])+(fr-x[i][2]-fr-x[j][2])*(fr-x[i][2]-fr-x[j][2]));
bin=(int)(distance/(d-cutoff/(d-nbin*1.0)));
d-dibond[i][j][bin]++;
}
//==end==edit by bodu 2011-12-25
if (d-fp)
{
fprintf(d-fp, %10.3f, fr-time);
}
rc = gmx_ana_nbsearch_pos_init(d-nb, pbc, d-refsel-p);
if (rc != 0)
{
gmx_fatal(FARGS, Neighborhood search initialization failed);
}
for (g = 0; g nr; ++g)
{
frave = 0;
for (i = 0; i sel[g]-p.nr; ++i)
{
frave += gmx_ana_nbsearch_pos_mindist(d-nb, sel[g]-p, i);
[gmx-users] (no subject)
Hello Gromacs users, I'm using a Buckingham potential for the nonbonded interactions in my system, so I have the following lines in my forcefield.itp file: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no 1.0 1.0 -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re:
I apologize for the truncated message; I pressed send too soon. According to the Gromacs manual, pairs cannot be generated automatically for the Buckingham potential, but the [ pairtypes ] directive seems to only accept parameters in LJ form (i.e. c6 and c12, instead of a, b, and c6). I've been looking into ways to interconvert between the two potential forms, but haven't found anything... Can anyone who has successfully generated a topology using the Buckingham potential shed light on this issue? Thank you so much, Olivia On Wed, Dec 28, 2011 at 11:05 AM, Olivia Waring owar...@princeton.eduwrote: Hello Gromacs users, I'm using a Buckingham potential for the nonbonded interactions in my system, so I have the following lines in my forcefield.itp file: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no 1.0 1.0 -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] -pbc nojump
Dear GROMACS users, I have a problem about trjconv -pbc nojump, I have 2 micelles in the end of my simulation. For analysis I should do three steps for micelle clustering at http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering?highlight=micelle+clustering Steps 1 and 2 work good and when I view my trajectory after step2 by : ngmx -f a_cluster.gro -s a_cluster.tpr is viewed 2 micelles, but when I did step 3 (trjconv -nojump) and after do : ngmx -f a_cluster.xtc -s a_cluster.tpr has been created 1 micelle and reminder of monomers have been collected as some groups at different places. May I ask you to help me, please? Thank you Best Regards Sara-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Ligand-Ligand interaction
I have been trying to set up simulation between 10 molecules of taurine with lysolecithin stearoyl, i generated the topology files with PRODRG but i s haven't managed to run the equilibrium. The error i recieve says there's a problem with the position restrain files. What can i do? Thanks in Advance Hovakim Grabski Russian-Armenian Slavonic University-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Ligand-Ligand interaction
Hovakim Grabski wrote: I have been trying to set up simulation between 10 molecules of taurine with lysolecithin stearoyl, i generated the topology files with PRODRG but i s haven't managed to run the equilibrium. The error i recieve says there's a problem with the position restrain files. What can i do? Without the exact error message, it's hard to help. Likely you've constructed the topology incorrectly. See the following: http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds Also note that PRODRG topologies are generally unreliable and require careful reparameterization. See the paper linked from: http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] -pbc nojump
Hi Sara, The problem is that your micelle is formed at the end of the trajectory. To get what you want, you need to mirror the trajectory, follow the procedure you followed, and mirror the resulting trajectory. I posted a piece of python code for mirroring a trajectory a while back: http://lists.gromacs.org/pipermail/gmx-users/2011-May/061443.html Hope it helps, Tsjerk On Wed, Dec 28, 2011 at 5:25 PM, mohammad agha mra...@yahoo.com wrote: Dear GROMACS users, I have a problem about trjconv -pbc nojump, I have 2 micelles in the end of my simulation. For analysis I should do three steps for micelle clustering at http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering?highlight=micelle+clustering Steps 1 and 2 work good and when I view my trajectory after step2 by : ngmx -f a_cluster.gro -s a_cluster.tpr is viewed 2 micelles, but when I did step 3 (trjconv -nojump) and after do : ngmx -f a_cluster.xtc -s a_cluster.tpr has been created 1 micelle and reminder of monomers have been collected as some groups at different places. May I ask you to help me, please? Thank you Best Regards Sara -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Coulomb Energies
On 12/17/11, Saba Ferdous saba.bsbi...@iiu.edu.pk wrote: Dear Gromacs experts, I want to ask about coulomb energies. Like if coulomb-SR and coulomb-14 show high RMSD then what should we interpret from such results?? Average Coulomb Energy (kJ/mol) -1.62657e+06 RMSD 2236.85 Error Estimation 150 Total drift (kJ/mol) -894.82 Many thanks -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Coulomb Energies
afsaneh maleki wrote: On 12/17/11, Saba Ferdous saba.bsbi...@iiu.edu.pk wrote: Dear Gromacs experts, I want to ask about coulomb energies. Like if coulomb-SR and coulomb-14 show high RMSD then what should we interpret from such results?? Average Coulomb Energy (kJ/mol) -1.62657e+06 RMSD 2236.85 Error Estimation 150 Total drift (kJ/mol) -894.82 This question has already been answered: http://lists.gromacs.org/pipermail/gmx-users/2011-December/067016.html -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Intel composer vs. Intel Studio
What performance are you getting that you want to improve more? Here's a datapoint from the last simulation I ran: Currently running gromacs 4.5.4 built with icc+fftw+openmpi on infiniband qdr and I get about 9.7ns/day on 64 PP nodes with 4 PME nodes (68 total 2.66ghz X5650) on my 99113 atom system in single precision I find that it is more important to optimize your PP/PME allocation than microoptimizing the code... I also find that at some point above 232 nodes (I don't remember what the exact number is), mdrun will complain about the overhead it takes to communicate energies if am having it communicate energies every 5 steps; which is a reflection on thea limitation of the infrastructure than the code too. On 2011-12-27 06:48:23AM -0600, Mark Abraham wrote: On 12/27/2011 11:18 PM, Sudip Roy wrote: Gromacs users, Please let me know what is the best option for gromacs compilation (looking for better performance in INFINIBAND QDR systems) 1. Intel composer XE i.e. Intel compilers, mkl but open MPI library 2. Intel studio i.e. Intel compilers, mkl, and Intel MPI library GROMACS is strongly CPU-bound in a way that is rather insensitive to compilers and libraries. I would expect no strong difference between the above two - and icc+MKL+OpenMPI was only a few percent faster than gcc+FFTW+OpenMPI when I tested them on such a machine about two years ago. Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] -pbc nojump
Hi Sara, Please keep discussions on the list. I'm not your private tutor. Whether you can do your analysis depends on the analysis you want to do. But if your aim is analyzing the formation of the micelle, you're probably better of reversing the trajectory. 1- trjconv -f md.trr -o md1.xtc -n index.ndx -pbc whole -s md.tpr This makes molecules whole, which is fine. Clustering should make molecules whole too, though, making this step redundant. 2- trjconv -f md1.xtc -s md.tpr -o cluster1.gro -e 60 -pbc cluster Fine, you get a cluster 3- trjconv -f cluster1.gro -s md.tpr -dump 150 -o cluster2.gro This does nothing special. Just because you have a reference clustered doesn't mean the output frame will turn out clustered. 4- grompp -f md.mdp -c cluster2.gro -o cluster1.tpr -n index.ndx 5- trjconv -f cluster1.gro -o cluster1.xtc -s cluster1.tpr -pbc nojump This screws up everything. You can only use -pbc nojump with a reference structure that is sufficiently close to the first frame of the trajectory. Your reference is a snapshot at t=600 ns. 6- trjconv -f cluster1.xtc -s cluster1.tpr -pbc mol -ur compact -center -o cluster3.xtc This would probably be fine if the trajectory was okay there. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] SPC density
On 28/12/11, Theodora García theodoraaagar...@gmail.com wrote: Hi I just saw the article Temperature Dependence of TIP3P, SPC, and TIP4P Water from NPT Monte Carlo Simulations: Seeking Temperatures of Maximum Density published in Journal of Computational Chemistry, Vol. 19, No. 10, 1179]1186 (1998). It gives 0.985 for SPC at 25 C with different setup... perhaps 0.978 is not so bad? Indeed. You should find the paper in which the parameterization of SPC was reported, and seek to reproduce the density reported there with a similar model physics. In general, a water model was probably parameterized to reproduce a set of observables reasonably well, and it does none of them perfectly. In practice, around 0.98 is normal enough in my recollection. Mark On Wed, Dec 28, 2011 at 9:34 AM, Theodora García theodoraaagar...@gmail.com wrote: Thank you very much for your advice... I have tried including dispcorr = enerpres in my mdp file and the density increased a bit in a timescale of 5 ns but it is still far from the value expected for pure water. These are the new results: Statistics over 251 steps [ 0. thru 5000. ps ], 3 data sets All averages are exact over 251 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 2982.675632.67534 2.70867e-05 0.135433 Volume 126.133 0.529594 0.529323 1.17324e-05 0.0586622 Density (SI)978.1144.106214.10412 -9.08266e-05 -0.454133 Heat Capacity Cv: 12.4733 J/mol K (factor = 8.06157e-05) Isothermal Compressibility: 5.40447e-05 /bar Adiabatic bulk modulus:18503.2 bar I guess I should get 1000 g/cm^3 Any other suggestion? On Tue, Dec 27, 2011 at 6:23 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-12-27 17:57, Theodora García wrote: Dear all I am starting some MD simulations aimed to calculate the volume of a solute in water as a function of the concentration. First I ran a simulation of a box with 4124 SPC water molecules (similar number of molecules that will be later used with my solute) for which I got the following results after ~7.5 ns: dispcorr = enerpres Statistics over 3762001 steps [ 0. thru 7524.0005 ps ], 3 data sets All averages are exact over 3762001 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 298125.156125.156 1.9202e-05 0.144476 Volume 126.90853.291753.2917 5.61522e-06 0.0422489 Density (SI)972.142408.201408.201 -4.30887e-05 -0.324199 Heat Capacity Cv: 16.9588 J/mol K (factor = 0.176389) Isothermal Compressibility: 0.543909 /bar Adiabatic bulk modulus:1.83854 bar Why am I obtaining so low density? The density seems to be constant over that timescale. This is my mdp file: constraints = all-bonds integrator = md dt = 0.002 nsteps = 250 nstxout = 5000 nstvout = 5 nstenergy = 1000 nstxtcout = 5000 energygrps = SOL nstlist = 5 ns_type = grid rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 coulombtype = PME fourierspacing = 0.15 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes Tcoupl = nose-hoover tau_t = 0.1 tc-grps = SOL ref_t = 298 Pcoupl = Parrinello-Rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 pcoupltype = isotropic gen_vel = yes gen_temp= 298 gen_seed= -1 Thanks in advance for any help... -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205(tel:%2B46184714205). sp...@xray.bmc.uu.se http://folding.bmc.uu.se(http://folding.bmc.uu.se/) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list.
Re: [gmx-users] Re:
On 29/12/11, Olivia Waring owar...@princeton.edu wrote: I apologize for the truncated message; I pressed send too soon. According to the Gromacs manual, pairs cannot be generated automatically for the Buckingham potential, Where does it say this? but the [ pairtypes ] directive seems to only accept parameters in LJ form (i.e. c6 and c12, instead of a, b, and c6). I've been looking into ways to interconvert between the two potential forms, but haven't found anything... Can anyone who has successfully generated a topology using the Buckingham potential shed light on this issue? You want a 1-4 interaction using Buckingham functional form? If so, I don't think GROMACS supports it. If you're trying to combine bits of force fields that use L-J with bits of force fields that use Buckingham, then that's almost certainly a bad idea. Mark Thank you so much, Olivia On Wed, Dec 28, 2011 at 11:05 AM, Olivia Waring owar...@princeton.edu wrote: Hello Gromacs users, I'm using a Buckingham potential for the nonbonded interactions in my system, so I have the following lines in my forcefield.itp file: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no 1.0 1.0 -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] how to use the modified gromacs 4.5.5's temple
On 28/12/11, 杜波 2008d...@gmail.com wrote: how to use gromacs 4.5.5's temple Dear teacher, i have already modify the code, and also make it. Attached is my modified code good. As you will see in the template code's desc variable, the original version needs to be told about several groups of atoms for its operation. Apparently you haven't changed that, so it prompts the user to get those groups. Of course, if you don't use them, then you can just enter any old selection (see the examples it suggests exist). Mark Dear teacher, how to use gromacs 4.5.5's temple? I expect that it is not meant to be functional. It's meant to be a template from which you can write functional code without having to work too hard on making it work like GROMACS tools work. Mark i make the temple successful! And when i run it (./template -f traj.xtc -s water.tpr -cutoff 2), the output like this: Reading file water.tpr, VERSION 4.5.5 (single precision) Reading file water.tpr, VERSION 4.5.5 (single precision) Specify a reference selection: (one selection per line, 'help' for help) help SELECTION HELP This program supports selections in addition to traditional index files. Please read the subtopic pages (available through help topic) for more information. Explanation of command-line arguments for specifying selections can be found under the cmdline subtopic, and general selection syntax is described under syntax. Available keywords can be found under keywords, and concrete examples under examples. Other subtopics give more details on certain aspects. help all prints the help for all subtopics. Available subtopics: cmdline syntax positions arithmetic keywords evaluation limitations examples thanks!! Regards, Bodu Department of Polymer Science and Engineering, School of Chemical Engineering and technology, Tianjin University, Weijin Road 92, Nankai District 300072, Tianjin City P. R. China Tel/Fax: +86-22-27404303 ; +8613820062885 E-mail: 2008d...@gmail.com ; dubo2...@tju.edu.cn -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Intel composer vs. Intel Studio
On 29/12/11, Peter C. Lai p...@uab.edu wrote: What performance are you getting that you want to improve more? Here's a datapoint from the last simulation I ran: Currently running gromacs 4.5.4 built with icc+fftw+openmpi on infiniband qdr and I get about 9.7ns/day on 64 PP nodes with 4 PME nodes (68 total 2.66ghz X5650) on my 99113 atom system in single precision It is very likely you can do better by following grompp's advice about having one-third to one-quarter of your nodes doing PME. See manual 3.17.5. I find that it is more important to optimize your PP/PME allocation than microoptimizing the code... Yes, hence the existence of g_tune_pme and other tools. I also find that at some point above 232 nodes (I don't remember what the exact number is), mdrun will complain about the overhead it takes to communicate energies if am having it communicate energies every 5 steps; which is a reflection on thea limitation of the infrastructure than the code too. I'd say this is more a reflection the limitations of the model you've asked it to use. Per manual 7.3.8 you can control this cost with suitable choices for the nst* variables. You can judge best whether you want faster performance or higher accuracy in the implementation of your approximate model... Mark On 2011-12-27 06:48:23AM -0600, Mark Abraham wrote: On 12/27/2011 11:18 PM, Sudip Roy wrote: Gromacs users, Please let me know what is the best option for gromacs compilation (looking for better performance in INFINIBAND QDR systems) 1. Intel composer XE i.e. Intel compilers, mkl but open MPI library 2. Intel studio i.e. Intel compilers, mkl, and Intel MPI library GROMACS is strongly CPU-bound in a way that is rather insensitive to compilers and libraries. I would expect no strong difference between the above two - and icc+MKL+OpenMPI was only a few percent faster than gcc+FFTW+OpenMPI when I tested them on such a machine about two years ago. Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] -pbc nojump
Thank you very much from your reply. Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 29, 2011 1:56 AM Subject: Re: [gmx-users] -pbc nojump Hi Sara, Please keep discussions on the list. I'm not your private tutor. Whether you can do your analysis depends on the analysis you want to do. But if your aim is analyzing the formation of the micelle, you're probably better of reversing the trajectory. 1- trjconv -f md.trr -o md1.xtc -n index.ndx -pbc whole -s md.tpr This makes molecules whole, which is fine. Clustering should make molecules whole too, though, making this step redundant. 2- trjconv -f md1.xtc -s md.tpr -o cluster1.gro -e 60 -pbc cluster Fine, you get a cluster 3- trjconv -f cluster1.gro -s md.tpr -dump 150 -o cluster2.gro This does nothing special. Just because you have a reference clustered doesn't mean the output frame will turn out clustered. 4- grompp -f md.mdp -c cluster2.gro -o cluster1.tpr -n index.ndx 5- trjconv -f cluster1.gro -o cluster1.xtc -s cluster1.tpr -pbc nojump This screws up everything. You can only use -pbc nojump with a reference structure that is sufficiently close to the first frame of the trajectory. Your reference is a snapshot at t=600 ns. 6- trjconv -f cluster1.xtc -s cluster1.tpr -pbc mol -ur compact -center -o cluster3.xtc This would probably be fine if the trajectory was okay there. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
