[gmx-users] Segmentation fault!!]

Eric Jakobsson jake at ncsa.uiuc.edu
Sat Mar 6 23:24:01 CET 2004

To look in different solvation layers, you have to do radial distribution 
function between each water molecule and the nearest protein atom.  For 
each water molecule, you can tell the solvation layer by the position of 
the first peak, and then do mean-square-deviation correlation function for 
the water molecules sorted according to solvation layer.  You need to 
repeat the radial distribution function at different times, to account for 
individual water molecules moving from one solvation shell to another.

Not trivial, but do-able.


At 01:37 AM 3/1/2004 +0530, you wrote:
>Dear Gromacs Error,
>While making the index file I split the non-protein part(I am doing
>simulation of protein in SPC water) into residues and selected around 1000
>water molecules and while cauculating the diffusion coefficient using
>g_msd command I encounter the following error
>Reading frame   0 time 0.000 Segmentation fault
>Please guide me why so??
>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. I have tried
>trjorder also but unable to do so. Please help me out of this problem.
>"You are making progress if each mistake You make is a new one"
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
405 N. Mathews Avenue
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909

(Currently on leave to NIH to serve as Director of Center for 
Bioinformatics and Computational Biology at the National Institute of 
General Medical Sciences and Chair of the NIH Biomedical Information 
Science and Technology Initiative Consortium.  Usual schedule is four days 
a week at NIH and three days a week at Illlinois.)

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