[gmx-users] Too close water molecules

David van der Spoel spoel at xray.bmc.uu.se
Mon Jan 5 16:07:00 CET 2004

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

> 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 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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