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 th
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 th
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:
http://www.gromacs.org/index.php?t
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 she
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, wrote:
> How can I do that using OPLSAA, because in the nb.itp file the
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
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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
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 simul
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
a...@ab-desktop:~/Masaüstü
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
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
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