[gmx-users] Segmentation fault!!]

[David van der Spoel]

On Sun, 2004-02-29 at 21:07, ankur gupta 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??
mismatch between input files, maybe? index file that specifies atoms
that are not in the trajectory...

> 
> 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.
> 
> sincerely
> Ankur
> 
> 
> 
> 
> "You are making progress if each mistake You make is a new one"
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-- 
David.
________________________________________________________________________
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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