[gmx-users] LINCS vs SHAKE
thompsjj at purdue.edu
thompsjj at purdue.edu
Mon Nov 1 03:15:21 CET 2010
I concur with Mark - you're pumping heat into the solvent which is
physically unsound, particularly at the solute-solvent boundary in
your situation. This would be analogous to making a block of metal at
900K instantly "appear" in water at 300K: what would happen?
Technically the Nose-Hoover thermostat is going to be better than
Berendsen at reducing the noncanonical bias in the replica exchange,
but of course using a smaller range of temperatures is going to reduce
the pressure on the thermostat to keep up with velocity scaling. This
is a different problem entirely, though. To be honest, I see the
difference in your management of protein and solvent temperatures as
the biggest problem here.
Quoting Mark Abraham <mark.abraham at anu.edu.au>:
>
>
> ----- Original Message -----
> From: Sai Pooja <saipooja at gmail.com>
> Date: Monday, November 1, 2010 10:24
> Subject: Re: [gmx-users] LINCS vs SHAKE
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
>> Some information:
>> Except for this note, I do not get any other warning when I
>> generate the .tpr files. The cut-offs are in line with the
>> forcefield recommendations and
>> The largest charge group contains 12 atoms.
>> Since atoms only see each other when the centers of geometry of
>> the charge
>> groups they belong to are within the cut-off distance, too large charge
>> groups can lead to serious cut-off artifacts.
>> For efficiency and accuracy, charge group should consist of a few atoms.
>> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc
>
> Probably not critical, but IIRC the latest GROMACS imposes
> single-atom charge groups for CHARMM, in line with CHARMM developer
> advice.
>
>>
>> @JJ
>>
>> I am currently using Nose-hoover and it does happen close to a
>> replica-exchange. Since I am attempting an algorithm which only
>> scales the temperature of the protein and not the solvent across
>> replicas, your pointer on the thermostat seems very pertinent.
>
> Yep. That's a prime source for problems - IIRC post-exchange
> velocities are rescaled globally, not group-wise. Even if the latter
> were implemented, you'd still have to reconcile the fact that your
> simulations constantly have heat flowing from the solute heat bath
> to the solvent heat bath via your system. Is that sound?
>
> Also, I'm not sure which temperature GROMACS is taking as the
> replica temperature, whether that is dependent on the order of the
> temperature-coupling groups in the .mdp file, and whether it
> shouldn't be regarding your situation as questionable/illegal and
> complaining at the grompp stage.
>
>> Do you think a weaker coupling algo like Berendsen might help
>> resolve this problem?
>>
>> I can also try using a smaller temperature range. I am currently
>> using 300-900K (with solvent set at 300 for all 6 replicas).
>> Perhaps if I use a smaller temperature range like 300-550, this
>> could be prevented?
>
> If that's the cause, then the answer is "probably", but you should
> address the underlying problem/question as above.
>
> Mark
>
>>
>> Pooja
>>
>> On Sun, Oct 31, 2010 at 7:13 PM, <thompsjj at purdue.edu> wrote:
>> Have you looked into changing the thermostat yet? Can you
>> determine if the malformed residues are a result of a recent
>> replica exchange? This continues to sound like an overheat that the
>> thermostat cannot handle. >
> >
> >
> >
> >
> >
> >
>> Quoting Mark Abraham <mark.abraham at anu.edu.au>:
> >
> >
> >
>> ----- Original Message -----
>> From: Sai Pooja <saipooja at gmail.com>
>> Date: Monday, November 1, 2010 8:12
>> Subject: Re: [gmx-users] LINCS vs SHAKE
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >
> > Yes, I understand that. But then this is a protein in water
> simulation with CHarmm forcefield and I cannot find a reason as to
> why does this happen(esp after variable number of steps)?
> >
>> MD integrates equations of motion. If the starting configuration,
>> or integration procedure is not well-formed, then atoms will
>> experience large forces and motions, which lead to more, which
>> eventually lead to a smoking pile of debris. See
>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up for
>> discussion and suggestions
> >
>> Mark
> >
> > I have checked the .pdb files generated for the steps where
> Lincs fails and it seems that H atoms for atleast 1 sidechain are in
> incorrect positions(usually clashing). There doesn't seem to be a
> good way of analyzing this error. If you have any suggestions I
> would be eager to try them.
> > >
> > Pooja
> >
>> On Sat, Oct 30, 2010 at 3:40 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> > >
>> >
> > Sai Pooja wrote:
> > >
> > For Replica exchange, is there any advantage of in using SHAKE
> over LINCS(other than the stepsize)?
>> I am running an REM simulation and the simulation stops after
>> running for variable number of steps (100000, 10000000 etc.)
>> because some bond moves more than 30 degrees and LINCS gives a
>> warning.
> > >
>> >
> > It has been said (check the archive) that LINCS is more stable.
> Just because you're getting LINCS warnings does not mean the
> constraint algorithm is to blame, it's just the first algorithm that
> fails when your model physics implodes.
> > >
> > -Justin
> > >
>> >
> > Pooja
> > >
> > --
>> Quaerendo Invenietis-Seek and you shall discover.
> > >
>> >
> > --
>> ========================================
> > >
> > Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >
> > ========================================
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