Re: [gmx-users] print out the velocities and forces using template.c

I have checked with gmxcheck and velocities and forces are output in .trr. I am playing template.c to try to learn more about GMX. I read gmx_traj.c, but not quite understand. Can you give me a example, for instance the flags to be set in template.c to read the velcocities? thank you Qiang On F

[gmx-users] energy group exclusions - are forces calculated?

hi, Short question: if I define energy group exclusions between, say, group A and B - will members of group A and B be completely invisible to each other, or is simply their interaction energy not calculated or recorded in the energy output? long version: I'd like to set up a simulation in which

Re: [gmx-users] gromacs 4.0 -np parameter?

SLIM H.A. wrote: Justin, Thanks, I am not familiar with gromacs, where could I find specific information about the differences between 4.0 and earlier versions. The manual and the -h flag of every command work pretty well, along with release notes: http://www.gromacs.org/content/view/181/13

RE: [gmx-users] Re: About entropic contribution to the potential of mean force

Dear Zgzhang, I am interested in your answer to your own question since I asked basically the same several months ago, could you explain it better? Angel. De: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] En nombre de Zhang Zhigang Enviado el: jueves, 27 de noviembre de 2008 04:28 a.m. Para:

[gmx-users] correct processing of #define statements by grompp in gromacs 4.0.2 requires exactly one space after #define

I have fixed the bug reported by Daniel Seeliger in the case of two similar defines on one line. The problem occurred because the second define was a substring of the first define. This is in CVS for 4.0.3. Cheers, -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept.

Re: [gmx-users] Re:Re: x2top

Hi, > > if i just use the topology of the sugar without the protein then the > simulations starts but the atoms are not moving during the simulation. they > are exactly at the same position in frame 1 and frame n. therefore had the > idea to use the build-in x2top function. so i would be glad to g

Re: [gmx-users] gromacs 4.0 -np parameter?

SLIM H.A. wrote: I have recenly built gromacs 4.0 using MPI, however grompp -h does not include a -np option. Does this indicate that it actually was not built for multiprocessor use? No, it is simply not necessary to pre-process with -np anymore. -Justin Thanks Henk Slim ___

[gmx-users] gromacs 4.0 -np parameter?

I have recenly built gromacs 4.0 using MPI, however grompp -h does not include a -np option. Does this indicate that it actually was not built for multiprocessor use? Thanks Henk Slim ___ gmx-users mailing listgmx-users@gromacs.org http://www.groma

Re: [gmx-users] Re:Re: x2top

Bernhard Knapp wrote: > Justin wrote: It looks like your coordinate file is from PRODRG; why not use PRODRG to generate a rough topology, and refine it according to the ffG43a1 parameters? The problem is that the sugar in in contact with a bigger protein complex and the PRODRG server i

[gmx-users] Re:Re: x2top

> Justin wrote: It looks like your coordinate file is from PRODRG; why not use PRODRG to generate a rough topology, and refine it according to the ffG43a1 parameters? The problem is that the sugar in in contact with a bigger protein complex and the PRODRG server is not willing to accept mo

RE: [gmx-users] How to calculate virial in gromacs-4.0?

Hi, Gromacs uses a more complicated, but also more efficient way to determine the virial. If you write your own program, I would the much simpler direct way of just calculating r x f in all the force loops. Gromacs 4.0 still always uses shift vectors, but in parallel the graph is not used. Berk

RE: [gmx-users] Box vector shifts number in x and y/z dimension

Hi, The b and c box vectors can be such that they both have as x component half the vector a x-length. Thus together they can cause a shift of 1 full x length and thus you might need 2 shifts along x. Berk > Date: Fri, 28 Nov 2008 09:41:31 +0800 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs

Re: [gmx-users] Re: Re: defination of cluster

f instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20081128/0f3a29db/attachment-0001.html

Re: [gmx-users] Fatal error with grompp(with detail process)

Jenny Hsu wrote: Hi all: I have a problem with grompp I want to making "POPC+protein" file and I search the archieve and follow the process 1.run pdb2gmx for protein only 2.add below parameters into my topology file #include "ffG53a6.itp" #include "lipid.itp" #include "popc.itp" 3.adjust the

Re: [gmx-users] Analyzing a trajectory split over multiple files

Just as a note most analysis tools have a -noxvgr option to output the results without any of the formatting information for grace. Also I still think the easiest way to solve your problem is to just initially use trjcat to concatenate your trajectory, then run the analysis on this. Tom --O

Re: [gmx-users] print out the velocities and forces using template.c

Hi Qiang, You'll have to check whether the frame contains velocities (fr.bV == TRUE) or forces (fr.bF == TRUE). Also make sure you set the flags right to read velocities/forces. Check the source of g_traj or trjconv for examples. Cheers, Tsjerk On Fri, Nov 28, 2008 at 10:33 AM, Mark Abraham <[E

Re: [gmx-users] print out the velocities and forces using template.c

friendli wrote: Dear all users, A silly question: I want to print out the velocities and forces in the trajectories using template.c. g_traj or gmxdump do that. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailma

[gmx-users] print out the velocities and forces using template.c

Dear all users, A silly question: I want to print out the velocities and forces in the trajectories using template.c. In template.c, the coordinates of atom n is in fr.x[n][XX]. Reading the trx.h, i see the x,v and f are defined in the same way. So I just change it to fr.v[n][XX] for velocit

Re: [gmx-users] Fatal error with grompp(with detail process)

Jenny Hsu wrote: Hi Tsjerk: One of my friends combines popc information into G53a6 that's why i try to use G53a6. If its not working, which force field should i choose? Have a look at some literature for simulations on systems similar to yours. See what they do and form your own opinions.

Re: [gmx-users] Fatal error with grompp(with detail process)

Hi Tsjerk: One of my friends combines popc information into G53a6 that's why i try to use G53a6. If its not working, which force field should i choose? Best regards, Jenny 2008/11/28 Tsjerk Wassenaar <[EMAIL PROTECTED]> > Hi Jenny, > > The files lipid.itp/popc.itp contain references to atom typ

[gmx-users] Re: Re: defination of cluster

gt; > please let me know, and thanks a lot for your help > > > > > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please sea

Re: [gmx-users] Fatal error with grompp(with detail process)

Hi Jenny, The files lipid.itp/popc.itp contain references to atom types which are not in the G53a6 force field; that combination just doesn't work. lipid.itp/popc.itp were written to be used with another force field. It's generally not a good idea to mix force fields. Cheers, Tsjerk On Fri, Nov