[gmx-users] Re: Please guide!!

David spoel at xray.bmc.uu.se
Sun Feb 29 23:08:01 CET 2004

On Sun, 2004-02-29 at 22:06, ankur gupta wrote:
> Dear Professor Spoel,
> Thank you very much for your help. I need your help in
> sorting out the things for me. while running the
> simulation of protein in SPC water molecules, I used a
> total of 2536 water molecules to obtain a
> solvation shell three to four water molecules thick in
> the periodic box and now I want to calculate the
> diffusion coefficient in all the solvation layer to
> see the effect of protein in solvent dynamics. Please
> guide me how should I select just enough water
> molecules present in different layers or how to write
> a code(if any!). I have tried many things but failed.
> Please help me out of this problem.

Hm, maybe trjorder should write out an index file rather than reordering
the waters. That way, you can take a structure at time 0 find the N
closest waters, and compute their D. This would need you to make some
changes on trjorder.

An alternative is to compute lifetimes of hbonds between water and
protein, and between water and water, and compare those. Small
disadvantage there is that g_hbond in 3.2 does not work on multiple
groups. I will fix it soon, for 3.2.1 or 3.2.2.

David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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