Re: [AMBER] CCL4 simulation

From: sudipta <>
Date: Wed, 18 Mar 2009 07:47:48 +0000

Thanks for your reply. Actually I have visualized the simulated file by VMD,
XLEAP. There I have found some bonds are broken. Yeah, I have given a
minimization ran of 20000 steps. After minimization, some vacuum has
created. I have also tried to do this simulation by other software (NAMD)
but still that was showing same problem. The bond energy and electrostatic
energy were showing NAN, bend and vdw interaction energies were showing some
value. NAMD also show same thing. It was showing large value of bond and
electrostatic energy. I have placed the CCL4 molecules in a FCC lattice.


On Wed, Mar 18, 2009 at 7:44 AM, David A. Case <>wrote:

> 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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Received on Wed Mar 18 2009 - 01:21:17 PDT
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