[gmx-developers] Segfault during EM in recent git version

Berk Hess hess at cbr.su.se
Wed Oct 7 12:56:32 CEST 2009


Because of the CH2 vsite issue I would advise always to use

My advise would simply be not to use cg with vsites.
Anyhow steepest descents is good enough for starting a simulation.
For other purposes one should not use vsites.


Jochen Hub wrote:
> Hi,
> thanks for your suggestions.
> I have played now a bit with steep and cg, with and without vsites,
> constraints = all-bonds, only hbonds, or none, and different proteins
> in water (and with lincs-order/iter and emstep), so pretty much
> everything I could think of.
> The problem seems to be a combination of things:
> 1) EM *with* vsites is sometimes unstable *without* applying any bond
> constraints (as you suggested, Berk). Quite often however, EM with
> vistes runs fine also without constraints.
> 2) conjugate gradient either with constraints or with vsites (or both)
> is less stable than steepest descent. That came as a surprise to me,
> since I usually had better experience with cg compared to steep.
> 3) Using constraints = hbonds usually more stable than constraints =
> all-bonds
> Therefore, I would probably suggest the following for EM with vsites:
> 1) First try EM without constraints wither with cg or steep. Probably
> steep is is more stable than cg.
> 2) Try steep (not cg!) with constraints=hbonds or all-bonds (and
> remember to use lincs-order >= 8 and lincs-iter 4-8, as pointed out in
> the manual/mdp comments).
> 3) Always use flexible water (-DFLEXIBLE)
> I do generally not recommend to use cg with constraints, either with
> vsites or not.
> So, thanks again for the help. I think I will also write a brief wiki
> site on that, so other people benefit from that struggling...
> Best,
> Jochen
> Berk Hess wrote:
>> Hi,
>> Steepest descents does run without too many Lincs warnings.
>> I don't see why you would want to run conjugate gradients on a protein
>> in water.
> I usually had better experience with cg compared to steep, that's why
> I typically stick to cg.
>> But if cg runs without virtual sites, it should also run with virtual
>> sites.
>> Have you checked if the same system does miminize properly with cg
>> without
>> virtual sites, but with constraints?
> I have tried that. cg does not run with constraints without vsites, so
> the constraints seem to be the main problem with cg. But cg with
> vsites and without constrains, may also be unstable (but less unstable
> than with constraints).
> Apparently, cg seems to have trouble with constraints (very often) and
> vsites (sometimes). So it is probably best to just stick to steep when
> having vsites, and then to try with or without constraints.
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-developers-request at gromacs.org.

More information about the gromacs.org_gmx-developers mailing list