[gmx-users] position restraint

mdrun? It seems to me that that's the only possible source as I didn't specify it anywhere. Thanks, -- Kun Huang Department of Physics, Rensselaer Polytechnic Institute. Troy, NY. 12180. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] Re: Cylinder Pulling output file pullx.xvg wrong

orm: > > ATOM 1 C C A 1 4.039 > > ATOM 2 C C A 1 3.97 > > > > Well, you've named your residues "C" and the component atoms "C" so there's > no > real confusion about anything. It's also not the source of your problems. > > g_x2top may

[gmx-users] Cylinder Pulling output file pullx.xvg wrong?

Dear Gromacs users: I am trying cylinder pulling as an option of umbrella sampling using gromacs 4.0.7. Things seem to work but I noticed that in the output file pullx.xvg, the referece group's postion is always 0. I don't think it is right. When I use position pulling, the reference position is n

[gmx-users] how gromacs calculate center of mass for broken molecules?

Hi everyone: How gromacs calculate center of mass for broken molecules? If the molecule is broken due to the pbc, where will the center of mass be? Thanks, Kun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] g_rdf has a huge memory leak.

Hi everyone: I am using g_rdf to calculate radial distribution function. However when I check the memory usage using top, it seems to me that the code has a huge memory leak. My system has 4GB memory but it usually has 40MB free memory left after the program finishes. Does anyone have the same pr

[gmx-users] Thanks for instruction on using xdr library

Hello everybody: I just received an email from Jussi Lehtola. I include : extern "C" { #include } in my source code, and it works. Thanks all. Kun ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Re: help needed for using xdr library

Hi, Actually the xdrfile_xtc.h file did include the xdrfile.h. And I also tried to include xdrfile_xtc.h directly in my source file. The link error is still there. I really don't know what's the problem because the make test command passed. On Mon, Aug 17, 2009 at 1:34 PM, Vitaly V. Chaban wrote

[gmx-users] help needed for using xdr library

Hello everyone: Recently I am trying to use the xdr library downloaded from gromacs org to read xtc files. However when I link my program with the library there is an error. When I ran the make test, all the tests were passed. Thus I think that the library should work just I don't know how to link