Hi, everyone. I am running gromacs, using force field G43a2. I just want to
make sure that, does the gromacs uses periodic boundary condition in my
simulation? Well, anyhow, where could I find a place to know what kind of
boundary condition the gromacs uses?
Thanks ahead.
Xiaoling Leng
--
gmx-us
Manual section 7.3 covers what all the of the .mdp settings do. One of them
covers PBC.
Mark
- Original Message -
From: Xiaoling Leng
Date: Thursday, October 7, 2010 18:22
Subject: [gmx-users] A simple question
To: gmx-users
> Hi, everyone. I am running gromacs, using force field G43a
On Wed, Sep 29, 2010 at 21:56, David van der Spoel wrote:
>
> After setting nstcalcenergy = 1 I get
> Density 996.894 1.2 3.85083 1.86718 (kg/m^3)
>
> In other words the bug can be circumvented by setting this variable to 1. I
> will file a bugzilla.
>
Is this bug in now? I c
Dear GROMACS users,
I try to compute energies of a small peptide-domain complex and of its
constituents using implicit solvent, so that I can get the binding Delta
E. I need the accuracy to be high enough so that I can reliably measure
the Delta Delta E between the wildtype peptide and a mutati
Ondrej Marsalek wrote:
On Wed, Sep 29, 2010 at 21:56, David van der Spoel wrote:
After setting nstcalcenergy = 1 I get
Density996.8941.23.850831.86718 (kg/m^3)
In other words the bug can be circumvented by setting this variable to 1. I
will file a bugzilla.
Is thi
Hi,
It's bugzilla 579:
http://bugzilla.gromacs.org/show_bug.cgi?id=579
Actually the title is wrong, the pressure was correct, the pressure scaling,
and thus the density, not.
Berk
> Date: Thu, 7 Oct 2010 12:28:15 +0200
> Subject: Re: [gmx-users] Re: Problem with pressure coupling
> From: ondrej
Hi,
thanks for fixing this, Berk. Silly me, I did not include RESOLVED
bugs in my original search and therefore missed it.
Ondrej
On Thu, Oct 7, 2010 at 12:38, Berk Hess wrote:
> Hi,
>
> It's bugzilla 579:
> http://bugzilla.gromacs.org/show_bug.cgi?id=579
> Actually the title is wrong, the pre
Well, this happens to everybody.
The search feature is bugzilla is far too complex.
We are considering switching to a more powerful and easier system.
Berk
> Date: Thu, 7 Oct 2010 12:41:17 +0200
> Subject: Re: [gmx-users] Re: Problem with pressure coupling
> From: ondrej.marsa...@gmail.com
> To:
Hi Ehud!
Your settings are correct.
However, you can also use domain decomposition with GB,
and I at least usually bypass the editconf stage, and do
pdb2gmx->grompp->mdrun, when you do not want any pbc.
/Per
7 okt 2010 kl. 12.29 skrev Ehud Schreiber:
> Dear GROMACS users,
>
> I try to comp
Dear Gromacs,
I have been calculating the self Diffusion constant of my system.
Surfactants in a different solvents of the same volume. After
simulation for 20ns I found the following data for the trajectory of
the mean square displacement.
# D[ TPA] = 0.2039 (+/- 0.0503) (1e-5 cm^2
Hi
In the post-processing ( analysis) code using gromacs trajectory, I access
force values on atom using fr.x[indx_atm][XX]. The confusion I have is that
" what force is it? is it the force before constraints ( fixed bonds) are
applied or is it the effective force due to atom-atom interactions plu
Dear Gromacs users,
This is an announcement for SwissParam, a web service that provides
topologies and parameters for small organic molecules, compatible with
the CHARMM all atoms force field, for use with the CHARMM or GROMACS
softwares:
http://swissparam.ch/
The server is fully automatic
Hi,
On 10/6/10 3:48 AM, Igor Leontyev wrote:
Szilárd wrote:
The beta versions are all outdated, could you please use the latest
source distribution (4.5.1) instead (or git from the
release-4-5-patches branch)?
The result is the same for both the distribution 4.5.1 and git from
the release-
Thanks for contributing!
I added a page about it on the Gromacs website:
http://www.gromacs.org/Downloads/Related_Software/SwissParam
Rossen
On 10/7/10 7:13 PM, Michel Cuendet wrote:
SwissParam, a web service that provides topologies and parameters for
small organic molecules, compatible wit
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