[gmx-users] Giving an initial velocity to a group of atoms

[Mark Abraham]

Hi,

You can use grompp to generate velocities, use editconf to turn the .tpr
into a .gro file, and then do some operation on the velocities (e.g. add
constants to various groups) but this won't help much in the condensed
phase, because of collisions. Pulling groups is a different matter - see
manual and tutorials.

Mark

On Sun, May 17, 2015 at 5:43 PM Jashimuddin Ashraf <
jashimuddin.ashraf23 at gmail.com> wrote:

> Thanks a lot for your reply Dr. Lemkul. It is working now. The velocities
> are matching exactly as I have given them in the .gro file.
>
> But as the velocities I am giving are not very well calculated, the results
> are not very useful. If i wanted to give a group of atoms a certain
> velocity with respect to another group of atoms in my system (for example,
> if i had a system with a protein and a CNT and I wanted to start the
> simulation with an initial velocity of the CNT with respect to the protein)
> what shoud I do?
>
> I understand that this is not an error related to GROMACS but it would be
> very much helpful for me if you could shed some light on the problem that I
> am facing.
>
> Thanks in advance.
>
> On Thu, May 14, 2015 at 10:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 5/14/15 9:12 AM, Jashimuddin Ashraf wrote:
> >
> >> <<<<<<<< Please ignore my previous message. >>>>>>>>
> >>
> >> Thanks again for your reply Dr. Lemkul. My files are uploaded here.
> >>
> >>
> >>
> https://drive.google.com/file/d/0B8p1k0KkNddyVXg4UDhyNmE5Njg/view?usp=sharing
> >>
> >>
> > You're generating velocities (gen_vel = yes).  That completely defeats
> the
> > purpose of specifying velocities.  Also note that using a finite cutoff
> for
> > Coulombic interactions is not generally sound.
> >
> >
> > -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
> >
> > ==================================================
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