That looks very strange. Please file an issue at
redmine.gromacs.orgincluding all your .tpr and .cpt, and assign it to
me.
Mark
On Thu, Dec 13, 2012 at 1:07 PM, Kenny Bravo Rodriguez <
ke...@mpi-muelheim.mpg.de> wrote:
> Hi all,
>
> and thanks Mark, Chris and Xavier for your comments.
>
> I fina
Hi all,
and thanks Mark, Chris and Xavier for your comments.
I finally managed to run the REMD simulation but i can not restart the
simulation or continue the simulation after it finished.
I tried with a test system and run two replicas for just 20 ps. After it
finished correctly i extended th
Virtual sites also have a hidden benefit - not only can you take a longer
time step, but the width of the distribution of PE is relatively wider, so
you can have higher exchange probability for the same temperatures.
Mark
On Tue, Nov 20, 2012 at 12:34 AM, Christopher Neale <
chris.ne...@mail.utor
Xavier is right, except that you can also reduce the size of your system. You
can take larger steps in temperature
if you have fewer atoms. If you are using a cubic system, you can move to a
rhombic dodecahedron.
Even constraining all bonds will help a bit here (vs. harmonic bonds).
There are
Well either you use more replicas or you reduce the temperature
range ...
There is no way around!
On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote:
Dear All,
i am trying to performed REMD simulations using Gromacs.
My question is concerning the temperature distribution and the
nu
Dear All,
i am trying to performed REMD simulations using Gromacs.
My question is concerning the temperature distribution and the number of
replica.
I need to run 24 replicas of my system with a temperature range of
290-400 K. How can I select the temperatures values for each replica?
I tried t
On 03/03/11, Jianguo Li wrote:
>
>
>
>
>
> Dear all,
>
> I'd like to do folding simulations of a short peptide on membrane surface
> using REMD using atomistic FF. But the problem is that membrane will disrupt
> at high temperatures. To maintain the membrane structure, I am thinking the
Dear all,
I'd like to do folding simulations of a short peptide on membrane surface using
REMD using atomistic FF. But the problem is that membrane will disrupt at high
temperatures. To maintain the membrane structure, I am thinking the following
two methods:
(1) To use different coupling temp
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