On 2/14/13 11:02 AM, Sebastien Cote wrote:
Dear Justin,
Thank you very much for your answer.
I did not take this as a criticism of implicit solvent model. I was just
wondering what was the origin of the limitations you were speaking of.
I did some small implicit solvent simulations, but I must say that I have not
thoroughly looked at the impact of cutoffs on energy conservation. I will be
careful about that.
About the bug for the implicit solvent code in GROMACS, is it only found in the
new version 4.6 or it is also present in earlier versions such as in the 4.5
series?
I only verified it in 4.5. I have not had the time or need to look into it for
4.6, though from other (somewhat related) discussions, I get the impression that
it still exists. If someone can prove that this is not the case, that would be
welcome news. It is my understanding that a more elegant bugfix is in the works.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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