Do you have the correct density? Chloroform should be about
1.47, if your nvt box is too big to provide that density
the behavior you describe is to be expected.
jim
On Wed, 28 Aug 2002, Sophia Kondratova wrote:
>I am trying to do an MD simulation in a chloroform box. After doing a
>minimization, the box looks normal (looking with the help of ptraj). When I
>try to equilibrate with nvt ensemble, the box does not look square anymore
>but with gaps and holes. The longer the simulation runs, the more missshaped
>the box looks. The iwrap=1, and also I have used the image command of ptraj
>(image center familiar). None of this changes the irregular shape of the box.
>The same thing happens after an npt equilibration. Does this have anything to
>do with the fact that I am trying to use chloroform?
>
>Any help would be greatly appreciated.
>
>
>Sophia Kondratova
>Chemistry Department
>University of New Brunswick
>Canada
>
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Received on Wed Aug 28 2002 - 07:35:50 PDT
