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 <[email protected]>:
----- Original Message -----
From: Sai Pooja <[email protected]>
Date: Monday, November 1, 2010 8:12
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users <[email protected]>
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 <[email protected]> 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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