[gmx-users] Problem in shifting ensembles( NPT to NVT)

shankari hariharan hariharanshankari at gmail.com
Fri Sep 5 04:22:34 CEST 2008

Dear gmx users,

I want to study the effect of interface on the crystal growth. I have a
problem in fixing the methodology for the simulation system which contains
saturated glycine solution and crystal surface. I discussed the methodology
as below.

1. Constructed a crystal surface and in the y direction, added saturated
solution of glycine (bulk solution is equilibrated using NPT for 5ns before
adding to the crystal surface). The system consists of 560 crystlline
glycine+80 solute glycine+1455 water

2. Performed the minimization by position restrainting all glycine

3. Run NPT for 200ps at 100K with position restraint on glycine molecules.

4. Run NPT for 200 ps at 298 K with position restraint on glycine molecules.

5. Followed by NVT (equilibration and production) ensemble for 10ns.

The problems are

1. the finel production (NVT) has very high negative pressure say around
-1000 bar.

2. the surface is not stable and dissolved into the solution which shouldn't

I think I have done some mistake in the shifting of ensembles. I will be
grateful to hear your suggetions for fixing the methodology.

Thanks for spending your valuable time.

With regards,

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