----- 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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