[gmx-users] Flat-bottomed position restraint set

[liuyong_1007 at dicp.ac.cn]

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:
#ifdef POSRES_WATER
; 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
#endif
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