[gmx-users] Re: Too close water molecules

[saurabh shakya]

I am using the opls force field and the cystines are
neutral .I have tried spc,flexscp and tip3pgmx type
water but the problem remains the same.

Regards
Saurabh 
On Mon, 2004-01-05 at 13:28, saurabh shakya wrote:
> Hi all,
> Wish you all a happy new year.
> I am running md simulation of a protein in water
.The
> md run for this protein runs absolutely fine in
vaccum
> ,but after i solvate it the water molecules tend to
> get too close (as close as 1.4 A) to a particular
> cystine group after few picoseconds of postion
> restrained md which results in a Lincs warning .
> The energy minimization runs successfully for the
> solvated system.

chekc the protonation state on the cysteine. Is it a
Cys- ? What force
field?

> I tried to delete these water molecules manually and
> continue the run but after few pico seconds again
> other waters were too close .
> Is there a way by which i could prevent the water
> molecules from getting too close to the cystines.
> All suggestions are welcome
> Thanks 
> Saurabh
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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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