[gmx-users] difference in rvdw , rlist parameters in em and nvt steps
sadr.mahboobe1989 at gmail.com
Thu Feb 11 11:57:29 CET 2016
It was very helpful... thanks a lot.
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On Feb 11, 2016 2:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
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.
> Best regards
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> On Feb 11, 2016 12:22 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> On Thu, Feb 11, 2016 at 9:46 AM Mahboobe Sadr <sadr.mahboobe1989 at gmail.com>
>> 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.
> Best regards
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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