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

[Jashimuddin Ashraf]

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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