[gmx-users] Giving an initial velocity to a group of atoms
Justin Lemkul
jalemkul at vt.edu
Sun May 3 18:24:30 CEST 2015
On 5/3/15 5:51 AM, Jashimuddin Ashraf wrote:
> 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
> ==================================================
> ============================================
>
You need to use proper formatting; check the .tpr with gmx dump to verify that
you're getting what you think you're getting.
> 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?
>
How are you assessing the success or failure of what you're doing? An MD
simulation will quickly diverge because of its inherent chaotic nature.
-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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