Samuel C Flores
samuel.flores at yale.edu
Tue Sep 5 16:17:50 CEST 2006
Can anyone point me to a tutorial on using REMD in Gromacs? I can't seem to
find anything on the web. There is a package called RPMDRUN, but I don't
see a reason to use outside packages when Gromacs, I believe, can handle
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Steven Kirk
Sent: Tuesday, September 05, 2006 3:43 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Energy minimization problem with macromolecule and
polarizable water model
I recently obtained (from DvS) the .itp file for the SSWM4-DP
polarizable water molecule, and a corresponding set of water box
I use double precision executables in all of the calculations mentioned
I ran an energy minimization on this box of water, then a 500ps run
(0.001ps timestep) at 300K with Berendsen pressure and temperature
coupling (pressure time constant set to 10 ps), PME, EnerPres dispersion
corrections, rlist=rcoulomb=rvdv=0.9. The shell particle was left massless.
Everything seemed to be OK in the run, total/kinetic/potential energies
settled nicely with no extreme fluctuations, density ended up about
998kg/m^3, no major temperature or box volume fluctuations.
So then I took the final water box and used genbox to solvate a charged
macromolecule with my shiny new water model, then added Na+ ions with
genion until charge balance was achieved.
I disabled the defaults line in the sswm4-dp.itp file, using instead
OPLS-AA defaults and force field parameters for everything that wasn't
Seemingly, so far so good.
The problem arose when I tried to energy minimise my solvated
macromolecule. Using the mdp settings:
cpp = /lib/cpp
constraints = none
integrator = steep
nsteps = 2000
; Energy minimizing stuff
emtol = 100
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1.0
coulomb-type = pme
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
lincs_iter = 4
the minimiser ran for about 100 steps, then converged to machine
precision. Unfortunately the max force was still very large (E+06, on a
water hydrogen). Reducing emstep and changing to the l-bfgs minimiser
(cg minimiser was disallowed because of presence of constraints,
presumably from the water model) had very little effect on the max force.
In desperation I even tried a 10ps full MD run at 10K to see if this
would ease the mysterious force problem a little, but got LINCS errors
on the very first step.
I'm now wondering if the problem is due to (working backwards):
a) Incompatible settings in my production system (solvated macromolecule)
b) genbox somehow mangling my equilibrated water molecules
c) Some mistake in my original equilibration of the box of polarizable
The LINCS errors suggest a structural problem, but if that arose in step
c), surely it would be visible as LINCS errors in the water box
equilibration run? This makes genbox my prime suspect.
I would be very grateful for anyone's opinions on where I have gone
wrong, and what I can do to fix the problem.
Many thanks in advance,
Dr. Steven R. Kirk <Steven.Kirk at hv.se, S.R.Kirk at physics.org>
Dept. of Technology, Mathematics & Computer Science (P)+46 520 223215
University West (F)+46 520 223299
P.O. Box 957 Trollhattan 461 29 SWEDEN http://taconet.webhop.org
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