[gmx-users] REMD in explicit solvent

[Esben Jannik Bjerrum]

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.

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.

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
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