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

[Jashimuddin Ashraf]

<<<<<<<< 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

On Thu, May 14, 2015 at 7:07 PM, Jashimuddin Ashraf <
jashimuddin.ashraf23 at gmail.com> wrote:

> Thanks again for your reply Dr. Lemkul. My files are uploaded here.
>
>
>
> https://drive.google.com/drive/u/1/folders/0B8p1k0KkNddyfkhaZEJDYTA1Y0wxcHh1UzlwOFB4TGVOZTNjVGZ0eGlaR2xKSGhwaUhIekk?ltmpl=drive
>
> On Thu, May 14, 2015 at 12:38 PM, Jashimuddin Ashraf <
> jashimuddin.ashraf23 at gmail.com> wrote:
>
>> Thanks again for your reply Dr. Lemkul. I am uploading my files here.
>>
>> On Tue, May 12, 2015 at 2:38 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> On 5/11/15 11:03 AM, Jashimuddin Ashraf wrote:
>>>
>>>> Thanks again for your reply Dr. Lemkul.
>>>>
>>>> I was also expecting a disaster because I gave an unrealistic starting
>>>> velocity of the structure. But the simulation was running fine. I tried
>>>> using the gmxdump and found that the velocities I am getting are not the
>>>> velocities I've given to the atoms.
>>>>
>>>> In your reply you were kind to reply that "You need to use proper
>>>> formatting
>>>> "
>>>>
>>>> I am following the format in the lilnk -
>>>>
>>>> http://chembytes.wikidot.com/g-grofile
>>>>
>>>> what I did was I just added 3 extra columns to my .gro file manually
>>>> after
>>>> getting .gro file from editconf. What might be my problem?
>>>>
>>>>
>>> Without access to all of your files, there's no way to know.  If you
>>> want to upload a tarball of your .gro, topology, and .mdp file, that will
>>> help.
>>>
>>>
>>> -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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>>
>