[gmx-users] virtual site - algorithmic reasons
samithzzz1 at gmail.com
Fri Apr 1 09:42:45 CEST 2016
okay thank you very much. I will try.
On Thu, Mar 31, 2016 at 4:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 3/31/16 6:06 AM, Samith Rathnayake wrote:
>> Hi everyone,
>> Recently i was used to started Bevan Lab tutorial and gone through
>> specially with virtual site tutorial.In this tutorial Dr.Justin emphasized
>> that co2 cannot effectively build in traditional sense because of
>> algorithmic reasons. And cant hold 180 degree during a simulation.Could
>> any one elaborate what are this "algorithmic reasons" ? any publication
>> upon this virtual site techniques in any gromos force field? and also
>> this algorithmic reasons ? And if it is okey to used this virtual site
>> techniques in gromacs 4.6.5 version ?
> There are mailing list posts about it; I forget the details but the long
> and short of it was that the fluctuations around a 180-degree angle lead to
> numerical instability in the code. IIRC that was fixed some time ago, but
> I would not expect 4.6.5 to work. Try the newest version and see if you
> can get away with a linear angle without any fancy work.
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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