On 15/02/2012 5:09 AM, J. Nathan Scott wrote:
Hi all,
I know there has been a *lot* of discussion on the mailing list on
using freezegrps and potential pitfalls, but after having read much of
this discussion the past couple of days and the manual I still find
myself with questions and problems I'm hoping someone can help with.
What I want to do, specifically, is have my protein frozen (*not* just
constrained with some large force, I need actual freezing of every
protein atom) but have the solvent still react to the frozen protein.
The purpose behind this is to compare the water behavior near a
particular part of a protein when it is dynamic and when it is not and
thereby learn something about the "communication" between protein and
solvent in this case. However, it seems that I'm not finding a
rational set of mdp options to allow this, at least not a set for
which dynamics will run with any speed. I have tried many of the
things people have discussed on the mailing list, including turning
off constraints, turning off pressure coupling, reducing the Protein
heat bath temperature to 0 K, and using energygrp_excl. Here are the
parameters I just tried:
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
integrator = md
nsteps = 1000000
dt = 0.001
nstxout = 1
nstvout = 1
nstxtcout = 1
nstenergy = 1
nstlog = 1
continuation = yes
constraints = none
dt = 0.0005 is normally used when there are no constraints.
ns_type = grid
nstlist = 5
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 0 300
pcoupl = no
pbc = xyz
DispCorr = EnerPres
gen_vel = no
freezegrps = Protein
freezedim = Y Y Y
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
This ran, but *incredibly* slowly (I'm using a single 32 processor
node, and only got 255 steps in 10 wallclock minutes). From the
discussions I've read on the mailing list it seems that PME is
somewhat less than ideal for simulations involving frozen atoms, but I
used PME for electrostatics in my non-frozen simulations and would
like to keep that consistent if possible (I do get a grompp warning of
course). I am also getting warnings in the log file like: "DD step
254 vol min/aver 0.183! load imb.: force 2395.3% pme mesh/force
1.243" which I believe must be due to the frozen protein causing
difficulties with domain decomposition.
Can anyone offer any advice regarding these issues? I know this has
been discussed often, but nothing I'm finding in the archives is
particularly relevant.
Allowing a run to complete and inspecting the timing breakdown at the
end of the .log file might be instructive. Manual 7.3.24 suggests the
use of energy group exclusions.
Mark
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