[gmx-users] Flat-bottomed position restraint set

liuyong_1007 at dicp.ac.cn liuyong_1007 at dicp.ac.cn
Wed Nov 12 14:52:41 CET 2014

Dear Gromacs users!

I use the flat-bottomed position restraints to avoid the molecules to escape from the clusters to the vacuum. The parameters of the restraints on water molecules are shown as follow:
; Position restraint for each water oxygen
[ position_restraints ]
;  i   funct       g         r(nm)       k
   1    2        1          3         30.0
   2    2        1          3         30.0
   3    2        1          3         30.0
However, water molecules still escape away from the cluster to the vacuum after about 100 ns MD run at 550K. What should be done with the restraints to avoid the water molecules to escape to the vacuum?
Best regards,
Yong Liu

liuyong_1007 at dicp.ac.cn

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