Dear GMX-users,
I am initiating a series of simulations of a dimeric protein in water, i.e.
something that should be fairly trivial. I use gromacs 4.6.5, vsites for the
hydrogens, amber99sb-ildn for the protein, and tip4p-Ew for the water. With a
time step of 0.004 I keep getting occasional
Hi Mark,
On Mon, Jan 20, 2014 at 3:01 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
Do you use this feature?
Yes, I do.
It's a great feature especially when I haven't used GROMACS in a while.
Do you use this feature with a shell other than bash?
No, just bash.
Jan
--
Gromacs Users
On Tue, Jan 21, 2014 at 10:23 AM, Djurre de Jong-Bruinink
djurredej...@yahoo.com wrote:
Do you use this feature?
Do you use this feature with a shell other than bash?
Yes, I use this feature and missing it would be a great loss to my workflow.
However, I only use it in bash. Is the
On Wed, Jan 22, 2014 at 5:50 PM, jkrie...@mrc-lmb.cam.ac.uk wrote:
I +1 shell completions too. It would be ok for me too if they were only in
bash. I think my default shell on the cluster may be tcsh but I can change
it to bash if necessary.
I'd be happy to try helping to implement it but I
Hi,
On Tue, Jan 21, 2014 at 11:23 AM, Djurre de Jong-Bruinink
djurredej...@yahoo.com wrote:
On a slightly related issue: the enviroment variable GMX_NO_CREDITS
doesn't work anymore in gmx5b. That made my work in the terminal a lot
easier too (Not that I think you guys don't deserve the
Hi,
On Wed, Jan 22, 2014 at 7:40 PM, jkrie...@mrc-lmb.cam.ac.uk wrote:
ok. I suppose I can try.
If you want to help, I suggest starting from the completion files generated
by https://gerrit.gromacs.org/#/c/2590/ (they get generated to
src/programs/completion when you run 'make completion').
1. could you please tell me what does this mean ? charge group is
inappropriately large the overall charge is appear to zero in my
topology. i am little confused here.
2. if below atoms types in represent C 111...so on and those atom types
appear in the error
Copls_240012.011
Why does trjconve need a tpr file for -pbc options?
Thanks!
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Btw, regarding symlink, I'd suggest that at least for mdrun it would
be nice to provide completion. This will also work for mdrun-only
builds.
--
Szilárd
On Wed, Jan 22, 2014 at 8:59 PM, Teemu Murtola teemu.murt...@gmail.com wrote:
Hi,
On Wed, Jan 22, 2014 at 7:40 PM,
On 22.01.2014 15:03, Jianguo Li wrote:
I have an doubt on the GPU hardware. Recently I heard from a nvidia person that
unlike Kepler card, GTX card does not have the memory check and correction. It
is no problem for gaming, but may lead to wrong results for scientific
computing.
Fermi,
Thanks.
So, trjconv alters the original .tpr file, adding the new periodic boundary
conditions?
On Wed, Jan 22, 2014 at 1:36 PM, Justin Lemkul jalem...@vt.edu wrote:
On 1/22/14, 4:33 PM, Rafael I. Silverman y de la Vega wrote:
Why does trjconve need a tpr file for -pbc options?
It is
On 1/22/14, 6:50 PM, Rafael I. Silverman y de la Vega wrote:
Thanks.
So, trjconv alters the original .tpr file, adding the new periodic boundary
conditions?
No, the .tpr is an input file and is not changed in any way.
-Justin
On Wed, Jan 22, 2014 at 1:36 PM, Justin Lemkul
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