[gmx-users] Giving an initial velocity to a group of atoms
Jashimuddin Ashraf
jashimuddin.ashraf23 at gmail.com
Sun May 3 11:51:16 CEST 2015
Thanks for your reply Dr. Lemkul. I was simulating a small carbon nanotube
to test the idea. So, I added three extra columns after the coordinates
inside my .gro file like this-
==================================================
============================================
Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm
64
1C C 1 10.539 10.000 10.061 1 0 0
1C C 2 10.534 10.070 10.183 1 0 0
1C C 3 10.539 10.000 9.817 1 0 0
1C C 4 10.498 10.206 9.939 1 0 0
1C C 5 10.534 10.070 9.939 1 0 0
1C C 6 10.466 10.269 10.061 1 0 0
1C C 7 10.498 10.206 10.183 1 0 0
1C C 8 10.381 10.381 9.817 3 0 0
1C C 9 10.466 10.269 9.817 3 0 0
1C C 10 10.328 10.427 9.939 3 0 0
1C C 11 10.381 10.381 10.061 3 0 0
1C C 12 10.206 10.498 10.183 3 0 0
1C C 13 10.328 10.427 10.183 3 0 0
1C C 14 10.139 10.520 9.817 3 0 0
1C C 15 10.206 10.498 9.939 3 0 0
1C C 16 10.000 10.539 10.061 3 0 0
1C C 17 10.139 10.520 10.061 3 0 0
1C C 18 9.930 10.534 10.183 3 0 0
1C C 19 10.000 10.539 9.817 3 0 0
1C C 20 9.794 10.498 9.939 3 0 0
1C C 21 9.930 10.534 9.939 3 0 0
1C C 22 9.731 10.466 10.061 3 0 0
1C C 23 9.794 10.498 10.183 3 0 0
1C C 24 9.619 10.381 9.817 3 0 0
1C C 25 9.731 10.466 9.817 3 0 0
1C C 26 9.573 10.328 9.939 3 0 0
1C C 27 9.619 10.381 10.061 3 0 0
1C C 28 9.502 10.206 10.183 3 0 0
1C C 29 9.573 10.328 10.183 3 0 0
1C C 30 9.480 10.139 9.817 3 0 0
1C C 31 9.502 10.206 9.939 3 0 0
1C C 32 9.461 10.000 10.061 3 0 0
1C C 33 9.480 10.139 10.061 3 0 0
1C C 34 9.466 9.930 10.183 3 0 0
1C C 35 9.461 10.000 9.817 3 0 0
1C C 36 9.502 9.794 9.939 3 0 0
1C C 37 9.466 9.930 9.939 3 0 0
1C C 38 9.534 9.731 10.061 3 0 0
1C C 39 9.502 9.794 10.183 3 0 0
1C C 40 9.619 9.619 9.817 3 0 0
1C C 41 9.534 9.731 9.817 3 0 0
1C C 42 9.672 9.573 9.939 3 0 0
1C C 43 9.619 9.619 10.061 3 0 0
1C C 44 9.794 9.502 10.183 3 0 0
1C C 45 9.672 9.573 10.183 3 0 0
1C C 46 9.861 9.480 9.817 3 0 0
1C C 47 9.794 9.502 9.939 3 0 0
1C C 48 10.000 9.461 10.061 3 0 0
1C C 49 9.861 9.480 10.061 3 0 0
1C C 50 10.070 9.466 10.183 3 0 0
1C C 51 10.000 9.461 9.817 3 0 0
1C C 52 10.206 9.502 9.939 3 0 0
1C C 53 10.070 9.466 9.939 3 0 0
1C C 54 10.269 9.534 10.061 3 0 0
1C C 55 10.206 9.502 10.183 3 0 0
1C C 56 10.381 9.619 9.817 3 0 0
1C C 57 10.269 9.534 9.817 3 0 0
1C C 58 10.427 9.672 9.939 3 0 0
1C C 59 10.381 9.619 10.061 3 0 0
1C C 60 10.498 9.794 10.183 3 0 0
1C C 61 10.427 9.672 10.183 3 0 0
1C C 62 10.520 9.861 9.817 3 0 0
1C C 63 10.498 9.794 9.939 3 0 0
1C C 64 10.520 9.861 10.061 3 0 0
20.00000 20.00000 20.00000
==================================================
============================================
but my simulation does not seem to have any effect of this. I tried
increasing the value but it did not change the results. How can I solve
this?
Thanks in advance.
On Sat, May 2, 2015 at 10:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 5/2/15 12:27 PM, Jashimuddin Ashraf wrote:
>
>> Dear Gromacs users,
>>
>> I was wondering if it is possible to give an initial velocity to any group
>> of atoms in GROMACS? I went through the manual but could not find any
>> suitable solution to it. Is the parameters related to "Velocity
>> generation"
>> in the .mdp file somehow related to this?
>>
>>
> No, those options are only for specifying whether or not random velocities
> should be generated.
>
> Velocities are read from .trr, .cpt, or .gro files. Writing the desired
> velocities in the .gro is likely the easiest approach.
>
> -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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