[gmx-users] CHCL3 box equilibration

Germana Paterlini germana at certusoft.com
Thu Feb 27 22:36:53 CET 2003

I had no luck so far in equibrating a CHCL3 box.
I tried two things.

1) I first started with a CHCL3 solvent box (borrowed from AMBER).
Minimiz is ok and NVT run appears ok. However, when I tried to switch to NPT,
I get the usual "pressure scaling more than 1%" error. As I understand, this is a sign that
the box is not equilibrated. I increased pressure coupling (up to 2.5), but it did not help.

What can I do next?
Note that, at the end of the NVT (up to 1 ns, 300K, Berendsen), "holes" appear in the box, while other regions
have higher density. I  increased the cutoffs to 1.7(thinking they are trying to evaporate) but it did not help. What am I doing wrong?

2) I tried to build the box myself using the genbox command, but apparently genbox does not recognize
VdW radia for CHCL3 and genbox generate molecules on top of each other.
The command is : genbox -ci chcl3.gro -nmol #  (where nmol is set to approximate the density of CHCL3).
What should I do? Should I add the CHCL3 atom types to the vdwradii.dat file?


Germana Paterlini

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