[gmx-users] CHCL3 box equilibration

David spoel at xray.bmc.uu.se
Thu Feb 27 22:07:13 CET 2003

On Thu, 2003-02-27 at 22:36, Germana Paterlini wrote:
> 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?

If you have holes it means the density is negative, and your system
wants to contract. Seeting tau_p to any value >= 1 (ps) should work
unless when there is a systematic error in e.g. your topology. Is the
energy reasonable? Try to compute DH vap
(DHvap = kT - Epot) in this case.

Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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