On 19/06/2012 5:55 PM, Esben Jannik Bjerrum wrote:
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.
All the advice of
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
and http://www.gromacs.org/Documentation/Terminology/Blowing_Up 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 :-)
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.
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.
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 = 1000
nstxout = 1
nstvout = 1
nstlog = 1
nstenergy= 1000
nstxtcout= 1000
xtc_grps = Protein
energygrps = Protein SOL
nstlist = 10
ns_type = grid
rlist= 0.8
coulombtype = PME
rcoulomb = 0.8
Most would regard this set of PME parameters (most of which are coming
from defaults) as too cheap to be effective.
Mark
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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