[gmx-users] How to calculate Pseudo dihedral angle as a function of time.

[Justin Lemkul]

On 1/16/14, 1:35 PM, Kartheek wrote:
> Hi everyone,
> I wanted to calculate pseudo dihedral angle as a function of time for a BDNA system. GROMACS g_angle gives dihedral as a function of time for only four connected atoms not for groups. I have defined four groups, each group consist of COM of set of atoms. defined as follows in plumed format g1,g2,g3,g4 are four groups(these are not connected). any help will be appreciated.
> g1
> 1998 1999 2001 2003 2004 2005 2006 2007
> 2375 2376 2377 2380 2381 2382 2384 2385 2386 2387 2388
>
> g2
> 1986 1989 1990 1993 1995 1996 2010 2013 2015
>
> g3
> 1949 1952 1953 1956 1958 1959 1980 1983 1985
>
> g4
> 1961 1962 1963 1966 1967 1968 1970 1971 1972 1976 1977 1978
>

There isn't a direct way to do this in Gromacs, but you could use some of the 
tools to do it.  g_traj -ox -com will plot the coordinates of each group over 
time, then some simple math can be used to give you the corresponding 
pseudodihedrals, but that's something you'll have to script yourself.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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