[gmx-users] polymer NVT

javier jus29 at psu.edu
Fri Jul 22 23:59:19 CEST 2005

Dear Gromacssss

 My system consist of 1 polymer chain, and I need to do NVT simulations, so
I need to fix the box size according to  my polymer density.
 But I really do not understand editconf?

My edit conf is: ediconf -bt cubic -f file.gro -o out.gro -d 0.5 -center

But in this way I do not get the right density, so I have tried:

ediconf -bt cubic -f file.gro -o out.gro -d 0.5 -density 1010

but the resulting  box vector lengths are a=4 b=7 and c=0.3.  Therefore I
only can use very small cutoffs due to the small c value.

And my polymer chain does not look like a Gaussian chain, and it is outside
of the cell.

So, do you have some idea?




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