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<div class="moz-cite-prefix">On 19/06/2012 5:55 PM, Esben Jannik
Bjerrum wrote:<br>
</div>
<blockquote cite="mid:1340092540.28361.17.camel@morse" type="cite">
<pre wrap="">Hi Gromacs Users
I'm new to list, but hope to get a little help from someone experienced
with setting up some replica exhange simulations in explicit solvent. It
keeps exploding after app. 50 to 200 ps simulation time. It runs fine up
to there, and then suddently one or a couple of atoms get unstable and
move to much between timesteps.</pre>
</blockquote>
<br>
All the advice of <a
href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation">http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation</a>
and <a
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a>
pertains to each individual system for REMD. In particular, you need
to equilibrate each replica under its conditions and not expect them
to tolerate a sharp jump in T and to pressure-coupling at the start.
The fact that you are using gen-vel = yes is proof that you have not
equilibrated yet :-)<br>
<br>
<blockquote cite="mid:1340092540.28361.17.camel@morse" type="cite">
<pre wrap="">
Heres what I have done.
Build the peptide in extended configuration in pymol.
Ran a 200 ps simulation with implicit solvent model to compact the
structure.
Generated a solvent box.
Equilibrated the system for 200 ps.
Generated a range of MDP file with varying temperatures and made
individual .tpr files
Ran the simulation with the switches -multi 16 -replex 1000
I tried to troubleshoot a little with lowering the dt and equilibrating
and minimizing more. Also tried different temperature coupling, as I'm
not sure what is the most appropriate for REMD simulations.</pre>
</blockquote>
<br>
Here's where your background reading comes in ;-) What's good for
normal simulations is generally good for REMD. There is a school of
thought that NVT REMD is not good because the pressure is
artificially high (but I haven't seen anyone demonstrate artefacts
from that), but NPT costs extra because the volume change affects
your PME load balance and accuracy.<br>
<br>
<blockquote cite="mid:1340092540.28361.17.camel@morse" type="cite">
<pre wrap="">
Is there something wrong with the parameters of the mdp file?
title = Yo
cpp = /lib/cpp
include = -I../top
define =
integrator = md
dt = 0.002
nsteps = 10000000
nstxout = 10000
nstvout = 10000
nstlog = 10000
nstenergy = 1000
nstxtcout = 1000
xtc_grps = Protein
energygrps = Protein SOL
nstlist = 10
ns_type = grid
rlist = 0.8
coulombtype = PME
rcoulomb = 0.8</pre>
</blockquote>
<br>
Most would regard this set of PME parameters (most of which are
coming from defaults) as too cheap to be effective.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:1340092540.28361.17.camel@morse" type="cite">
<pre wrap="">rvdw = 0.8
tcoupl = Berendsen
tc-grps = Protein SOL
tau_t = 0.1 0.1
ref_t = 300 300
Pcoupl = Berendsen
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = 173529
constraints = all-bonds
Best Regards
Esben
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