Dear all amber users
I'm doing NVT simulation with pure water system.
The system size is about 30 cubic Angstrom and there are about 800
water molecules.
The periodic boundary condition is applied to the simulation.
POL3 watermodel was used.
I made the prmtop and inpcrd file using xleap, with leaprc.ff02polEP.r1
file.
I first did NPT simulation to get realistic water density,
and after that the NVT simulation was done.
The problem is, when I check the NVT result with visualization program
(I use VMD),
I can see sudden and rapid configuration changes for whole system.
I recorded the result and uploaded the video on youtube. Please check
the video first.
(
http://youtu.be/JpkKtBFTHEk )
Here the small triangles are watermolecules and the blue rectangular
box is unit cell.
The video is recorded in xy-plane, orthographical view.
At 2sec, 5sec, 6sec, 7sec, 10sec, 21sec, and 22sec, you would see what
I mean.
I first thought this might comes from the "nscm" option that removes
translational or
rotational move of center-of-mass, but after I set nscm = 0, still it
happens.
Could anyone tell me why such chanages happen or how can I get the
result without that?
I would really appreciate for any of your opinions.
Many thanks in advance,
yjLEE
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 30 2014 - 02:30:03 PDT
