[gmx-users] numerical matrix from xpm file

Hi all Is it possible to obtain the matrix in numeric form from xpm (obtained from gromacs analysis) files. because it's not coming in options for ourput files. thanks with regards anupam -- -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed

Re: [gmx-users] gromacs synaptic package manager

Hi, When I run the pdb2gmx, it is giving the error as folllowing. What can I do? Thanks in advance a...@ab-desktop:~/Masaüstü/gromacs-4.5.1/src/kernel$ pdb2gmx -h The program 'pdb2gmx' is currently not installed. You can install it by typing: sudo apt-get install gromacs bash: pdb2gmx: command

Re: [gmx-users] gromacs synaptic package manager

http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions#Getting_access_to_GROMACS_after_installation -Justin ahmet yıldırım wrote: Hi, When I run the pdb2gmx, it is giving the error as folllowing. What can I do? Thanks in advance

[gmx-users] Dispersion correction in a heterogeneous system

Dear gmx-users, Although this task has been already discussed few years ago (http://lists.gromacs.org/pipermail/gmx-users/2007-January/025668.html) the full summary is not clear to me. So I would really appreciate if somebody could give me advice on the following subject. I am trying to

Re: [gmx-users] gromacs synaptic package manager

ahmet yıldırım wrote: I can not pass to pdb2gmx. (can you look at the attached photo). I think you need to spend some time understanding how Linux/Unix commands work. You're attempting to cd pdb2gmx, and you're being told very clearly that pdb2gmx is not a directory. It's an executable,

[gmx-users] Gromacs opening intern position?

Dear Developers Is there any workshop for Gromacs planned in 2011? Do you know any opening intern position somewhere in Europe? Thanks in advance S. Mohammadi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] LJ potential

Be careful if you are going to change the parameter to zero , because there is a combination rule that defines the usage of C6 and C12. and this combination rule is defined in the *.itp file On Mon, Sep 27, 2010 at 8:34 PM, nishap.pa...@utoronto.ca wrote: How can I do that using OPLSAA, because

[gmx-users] Re: resolved pdb2gmx

Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. See comments inline below. ahmet yıldırım wrote: Hi, You said Per the instructions I sent before, you need to either add the location of your Gromacs installation to your PATH (in whatever

[gmx-users] Re: resolved pdb2gmx

As I said before, please keep all correspondence on the gmx-users list, for the benefit of the community, and perhaps the chance that someone else will have some helpful insight for you. I do not know what else to tell you. The instructions are very clear:

[gmx-users] Re: NAMD simulation in Gromacs

Dear Dr. Roland Schulz,   Thank you very much for your attention. I have Amber type ff  that includes bond, angle, dihedral and nonbounded interaction terms in Charmm file format. Should I use the patch to generate a gromacs topology from psf file ?   I have NAMD created.coor and .vel files

[gmx-users] Split pmf

Hello, dears gmx-users! I posted a message, but didn't get a response, it was my first one, so may be I did something wrong. Anyway, here it is: I've already run md and got pmf and it's correct. But I want to get not just a pmf of total force, but several profiles each of which corresponds to