[gmx-users] Too close water molecules

saurabh shakya shakya_79 at yahoo.com
Mon Jan 5 13:30:02 CET 2004

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.
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

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