[gmx-developers] Segfault during EM in recent git version
jochen at xray.bmc.uu.se
Wed Oct 7 13:14:01 CEST 2009
Berk Hess wrote:
> Because of the CH2 vsite issue I would advise always to use
For the CH2 issue, constraints=all-bonds helps indeed. In rings,
however, (phe and tyr) the EM trajectory may look very odd. The rings
are frequently not planar during the EM, also with steepest descents.
Apparently, the EM steps lead to configurations in the rings that cause
some trouble in lincs. That's why I suggested to try EM first without
Btw, with constraints=hbonds these rings remained planar, but the C-C
bond lengths may substantially fluctuate.
> 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:
>> 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 =
>> 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...
>> Berk Hess wrote:
>>> 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
>>> Have you checked if the same system does miminize properly with cg
>>> 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.
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Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
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