Dear Gromacs users,
I use Gromacs 4.5.1. The problem relates to the restarting procedure of a run.
Usually I restart the run with the -append option and now I need to move the
.trr and .xtc files to another directory since they got too big for the
directory quota where they were located by
On 12/23/12 3:21 AM, Davit Hakobyan wrote:
Dear Gromacs users,
I use Gromacs 4.5.1. The problem relates to the restarting procedure of a run. Usually I restart the run with
the -append option and now I need to move the .trr and .xtc files to
another directory since they got too big for
Dear gmx-users,
I would like to select, for each residue of a model, the residues that are
within 3.6 A in average over a simulation.
g_mdmat must create this information at some point while generating the
contact diagrams, but I would like to extract the real values before they
are
Dea GROMACS Users,
I want to calculate the free energy for my system, for example (Gibbs and
Helmholtz), but I didn't define the free_energy in the md.mdp and my simulation
has been finished!!!
May I ask you that say me is there a solution fro this problem?
Best Regards
Sara
--
gmx-users
by the way it's also interesting to me if there are any other possible
ways to obtain representation of the free energy surfaces in the
essential coordinates subspace ? Might the methods like Ubrella
sampling ( with applied PMF in the pulling direction along selected
eigenvector ) or flooding
Albert mailmd2...@gmail.com wrote:
Dear all:
As we know that many membrane has a membrane potential with typical
range from -40mV to 80mV. I am just wondering is it possible to add
voltage for membrane protein simulation in Gromacs? If yes, and how? I
go through the .mdp documentation and
Yun Shi yunsh...@gmail.com wrote:
Interesting. Would that be like adding sodium chloride on one side of
the membrane while adding only potassium on the other side?
On Sun, Dec 23, 2012 at 8:37 AM, Peter Lai p...@uab.edu wrote:
Albert mailmd2...@gmail.com wrote:
Dear all:
As we know that
Am 23.12.2012 21:05, schrieb Peter Lai:
You can have a look at http://www.ncbi.nlm.nih.gov/pubmed/21843471 ,
maybe that does what you want.
Best
Martin
Yun Shi yunsh...@gmail.com wrote:
Interesting. Would that be like adding sodium chloride on one side of
the membrane while adding only
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