[gmx-users] LINSC WARNING
jalemkul at vt.edu
Fri May 22 22:20:18 CEST 2015
On 5/22/15 10:46 AM, Ahmet Yıldırım wrote:
> I haven't tried vsites on GPU. I just used them for the united atom ffs
> (espically GROMOS ffs) with reaction field method. Actually I didn't get
> good results about the ligand in the system. Maybe the problem was force
> field (54A7) I used. Because for GROMOS ffs there is another problem that
> is helix melting :).
If helices are falling apart in 54A7, something else is going on. 53A6 has
known deficiencies there, but they were fixed in 54A7. Might even be too stable.
> 2015-05-22 16:08 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
>> On Fri, May 22, 2015 at 3:57 PM Albert <mailmd2011 at gmail.com> wrote:
>>> that's interesting.
>>> How about the ligand in the system? The hydrogen should also be treated
>>> in virtual site? Is it possible treat the binding pocket as explicit
>>> atoms, and all the rest in virtual hydrogen?
>> You're probably thinking of united atoms, which are entirely distinct. You
>> can read all about virtual sites in the manual and publications ;-)
>> Does it support GPU?
>> thx a lot
>>> On 05/22/2015 03:51 PM, Ahmet Yıldırım wrote:
>>>> Hi Phan,
>>>> If you want to use the time step of 4 fs, you can try to use "virtual
>>>> sites" (gmx pdb2gmx -f ... -vsite hydrogens). Please look at the
>>>> web site.
>>>> Virtual sites:The use of virtual sites offers another possibility to
>>>> increase the efficiency of the simulation. These are used to replace
>>>> hydrogen atoms, removing the fastest vibrations in the system that
>>>> otherwise limit the time step that can be used. Simulations run with
>>>> virtual sites can therefore use a time step of 4 fs, instead of the 2
>>>> that is used for simulations with explicit hydrogen atoms
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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
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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