[gmx-users] REMD simulation
mark.j.abraham at gmail.com
Tue Nov 20 22:56:41 CET 2012
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.
On Tue, Nov 20, 2012 at 12:34 AM, Christopher Neale <
chris.neale at mail.utoronto.ca> wrote:
> 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 lots of papers on this topic.
> To see why you don't get any exchanges, construct histograms of your
> potential energies and you will see
> that they don't overlap. Also, it is inefficient to take evenly spaced
> temperatures. This is not your major problem,
> but read a bit on exponentially spaced temperatures for REMD.
> -- original message --
> 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
> > 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 the server http://folding.bmc.uu.se/remd/index.php but for
> > my system it gives 50 replicas. If i try to take 24 evenly spaced
> > values from the obtained list of temperature then
> > the replicas do not exchange at all.
> > I am using Gromacs 4.5.5 and my system has 6862 water molecules and
> > 535 atoms for the solute.
> > Thanks in advanced
> > Kenny
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