Sai Pooja wrote:
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)? 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.
There have been a number of replies to your question that have provided good
ideas for you to investigate. Something about your system is becoming unstable,
but without seeing your .mdp file there's nothing but guesswork to be done.
-Justin
Pooja
On Sat, Oct 30, 2010 at 3:40 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto: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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
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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