[gmx-users] Questions regarding usage of the covariance analysis

[Justin Lemkul]

On 2/28/15 1:21 PM, James Starlight wrote:
> Dear Gromacs users!
>
> Here I'd to ask some methodological question regarding usage of
> g_anaeig and g_shame utilities for the calculation of the principal
> modes, projection of the trajectory on its plane and calculation of
> the free energy landscape along it.
>
> 1) Is it possible to automatically provide some input file for each
> execution of the g_anaeig consisted of the value correspond to the
> group number in the index.ndx file ? Here I need to perform many
> executions of the g_anaeig to calculate PCs from some atom subsets
> defined in the index.ndx and I would not to chose the group manually
> each time.
>

http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

> 2) Is it possible to improve quality (resolution) of the colored free
> energy diagrams made by
> g_sham –f 2dproj_1_2.xvg –ls gibbs.xpm -notime
> xpm2ps –f gibbs.xpm –o gibbs.eps –rainbow red
>

g_sham -ngrid

-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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