----- Original Message -----
From: Sai Pooja <saipo...@gmail.com>
Date: Monday, November 1, 2010 10:24
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users <gmx-users@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, <thomp...@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.abra...@anu.edu.au>:
>
>
>
----- Original Message -----
From: Sai Pooja <saipo...@gmail.com>
Date: Monday, November 1, 2010 8:12
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users <gmx-users@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 <jalem...@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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