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

[Jashimuddin Ashraf]

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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>
>