David Mobley schrieb:
Hi David,
enough and risks not being able to find the minimum. The smaller the
steps are the more accurately it should be able to find the minimum.
mmh, just my 0.02€: I guess in a very rough energy landscape (as in
solvated peptides or proteins) this is not generally true, because
with small steps the system might get stuck in the next tiny local
minimum, while with a larger step size it may jump across it.
And I guess exactly this happens in your failing simulations: Your
system is stuck in a local minimum high up on the slopes of the energy
funnel. I guess this is just normal and happens some times. You might
alter the system by a little modeling (move the problematic atoms
slightly), or try -DFLEXIBLE, or perhaps rather increase step size.
Double precision minimization has proved to be more stable for me in
problematic cases, like straightening out a skewed average structure
of a trajectory.
Regards
Christian
Thanks,
David
Best
XAvier
> 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
> huge?
>
> 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.
>
> Thanks,
> David
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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