[gmx-users] virtual site - algorithmic reasons

[Samith Rathnayake]

okay thank you very much. I will try.

- samith

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
>> about
>> 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
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>