AMBER Archive (2009)

Subject: Re: [AMBER] CCL4 simulation

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Mar 17 2009 - 21:14:51 CDT

On Tue, Mar 17, 2009, sudipta wrote:

> I want to do a simulation of CCL4 box by amber. To do this job, I
> have arranged 900 CCL4 molecule in a box of dimension 30.0, 30.0, 160.0 A.
> The density of that liquid is ~1.56 gm/cc. The force field parameter was
> generated from general amber forcefield file (gaff.dat) and .frcmod file by
> using xleap. The newly generated .prmtop and .inpcrd files were used for our
> simulation. But strangely I have found, after few thousands steps, the CCL4
> molecule has broken. I have checked in .prmtop file that the number of
> bonds, bends, charges, masses are correct but all atoms show same radius.
> please find herewith the attached .prmtop file generated for single CCL4
> molecule. please suggest me, how to overcome this problem.

It looks like all the bonds are there that should be there. How did you
determine that the molecule had "broken"? Does the bond energy become
very high? Does the temperature also blow up? Did you minimize the
structure before starting MD? etc.

You can probably guess by the questions above that we don't have enough
information to help very much. You should look at a water simulation
(e.g. in $AMBERHOME/test/4096wat) and compare things to your simulation
to look for clues. My best (wild) guess is a bad starting configuration
that was never able to settle down, but that's a pretty wild
extrapolation from little data....

...dac

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