[gmx-users] high repulsion in packed system

chris.neale at utoronto.ca chris.neale at utoronto.ca
Mon Jul 12 04:15:18 CEST 2010

Dear Shuai:

When you get some advice, it's useful if you can try it before coming  
back to the list.

Vitaly was simply giving you an idea about how to proceed. You need an  
initial state that it high-density and this is one way to get such a  
state fairly easily: start with a low density (by simply expanding the  
box) and then slowly increase the density (with pressure coupling).  
Figuring out the pressure that you should use is probably up to you.

If you don't understand how to enlarge the box size then you should  
probably hit the gromacs manual for a bit.


-- original message --

Dear Dr Chaban,

Thanks for your reply. If I do NPT to compress the box to the initial size
(small) EM works perfectly ?

I dont exactly realize the justification behind what you said. You mean I
have to change the pressure in mdp file which gives the box size I want?

Later, I need to perform actual NPT and NVT simulations with this packed
system. Can I not do NVT with this density?


In "PE60-3.75nm3.gro" enlarge the box size. Then use NPT simulation to
compress the MD box.
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