On 2/11/16 5:28 AM, M S wrote:
I thought the tutorial set the em parameters lower than nvt parameters based
on a specific reason. So there is no specific reason in tutorial?
No. Generally I aim to keep them the same throughout, for consistency. In this
case, it's just an oversight, but one that produces no practical detriment. As
Mark says, for the purposes of EM, it works. And I have, in fact, tested that
you get plausible results during EM even with different cutoffs. Not generally
a wise practice to be toying with such things, but for EM there is no real
problem. During dynamics is a whole other story.
-Justin
Best regards
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On Feb 11, 2016 12:22 PM, Mark Abraham <[email protected]> wrote:
Hi,
On Thu, Feb 11, 2016 at 9:46 AM Mahboobe Sadr <[email protected]>
wrote:
Dear all users,
In mdp files in ligand tutorial, rvdw,rlist.are equal to 1 in em step,.
And are equal to 1.4 in nvt,npt and production md
When we can set different interaction parameters for different step?
You should choose such parameters based on those used for the
parametrization of the force field, and/or subsequent reports of successful
applications of them, particularly by the original authors.
As you no doubt learned from the tutorial, EM is commonly used for relaxing
inconsistencies in the starting geometry so that equilibration can proceed
stably. Experience shows that short-range settings that are ultra faithful
to the force field do not materially improve the success of equilibration -
anything normally does the job fine.
Mark
Best regards
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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