[gmx-users] minimization -- bugzilla or general advice?

David Mobley dmobley at gmail.com
Wed Mar 26 21:06:32 CET 2008


I often have problems with minimization in gromacs, but now I think I
have something a little more systematic to say.

First, my system: I am simulating a short peptide in a mix of two
co-solvents. I use a program called packmol which can start pack
specified number of molecules into a box of specified size, with a
specified distance tolerance between atoms, to generate starting gro
files. I am simulating a number of variants of this peptide in various
mixes of the two co-solvents (one of which is water).

The problem I am having is that, even in double precision, gromacs
fails to properly minimize some of the systems -- minimization using
any of the minimizers I've tried (including steepest descents, my
preference) often terminates early (i.e. after ~50 steps) even in
double precision, leaving really large forces on some of the atoms
(usually 10^10 or more). The largest forces are usually on one atom of
a water molecule. Hence, when I plug the minimized output into
equilibration, my simulations explode due to large forces.

Small tweaks to the system can change whether minimization works
properly or not in some cases -- for example, switching from double
precision to single precision will make some systems which fail in
double minimize properly, as will changing cutoffs. I assume also
things like changing architectures will allow some systems to minimize
(I've seen this behavior in the past).

The problem is, I can find no combination of settings which will allow
*all* of my systems to minimize properly. Inevitably some fail, and I
end up having to go in by hand, look at the minimization log file, see
which water molecule has the huge force on it, and tweak its position
slightly by hand in the input gro file. Typically then minimization
will proceed just fine.

This brings me to my question: Are the minimization algorithms
truncating some of the forces at some threshold value or something?
That is, why does minimization often end even though forces are still

Currently, I'm using steepest descents with constraints turned off,
double precision, and emstep = 1.0e-8. I'm using Gromacs 3.3.2, rlist
= 0.9 = rcoulomb, rvdw-switch = 0.75 and rvdw = 0.8, pme_order 4,
ewald_rtol = 1e-04, and fourierspacing = 0.12, DispCorr = AllEnerPres,
and switched vdw.

Any tips will be appreciated. Having to tweak coordinates by hand (or
write a script to do it) to get things to minimize isn't really a
satisfactory solution for me.

I could submit a bugzilla, but I imagine what will happen if I submit
the cases that don't work for me is that they'll work fine for whoever
addresses the bugzilla and so this won't be regarded as a real
problem. Alternatively I could submit a whole slate of starting system
configurations and someone can debug just the ones that fail for them.


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