[gmx-users] REMD in explicit solvent
Mark.Abraham at anu.edu.au
Tue Jun 19 10:57:01 CEST 2012
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
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
> 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 = 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
Most would regard this set of PME parameters (most of which are coming
from defaults) as too cheap to be effective.
> 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
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