[gmx-users] changes of orientation with respect to time

[Justin Lemkul]

On 10/12/16 1:16 PM, Nikhil Maroli wrote:
> Dear all,
> I have a nanotube embed perpendicular to the  lipid bilayer , I would like
> to observe is there any changes in the orientation of tube with respect to
> initial position (the deviation from the perpendicular position/time)
> during the simulation . Can I find any gromacs tools for the same ?
>
> I'm not sure the possibilities of gmx angle  becuase of - It should be
> noted that the index file must contain atom triplets for angles or atom
> quadruplets for dihedrals. If this is not the case, the program will crash.
> )!
>

You want gmx gangle -g1 angle -g2 z

-Justin

-- 
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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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