[gmx-users] Cluster pb

nicolas Dinter dinter at rc.m-kagaku.co.jp
Tue May 25 05:20:20 CEST 2004

Dear cromacs users,

I am trying to build a 120 benzene molecule 3 3 3 box, but I had some
 So I have tried to change the time step (from 0.002 to 0.0000002) and
change the emstep (from 0.02 to 0.00002) bur it gave the same results (with
 I have also tried to build a larger box (5*5*5),where there is not any
overlap, and run energy minimisation, equilibrium researh with pressure and
temperature berendsen coupling (to get the good box size and density ), and
benzene form clusters.

On article (MD simulation studies of benzene...,Bull. Korean Chem. Soc.2002,
vol.23,no.3, p441-446) I saw that at 293.15 K, for a 120 molecule system,
the density is 0.8787 g/cc and the box size is 2.607nm.

So I am quite surprised by my results, could someone clarify my situation?
How can I prevent cluster from forming?


Nicolas Dinter

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