AMBER Archive (2007)

Subject: Re: AMBER: TIP4P MD simulations

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 09 2007 - 13:31:15 CDT

On Mon, Jul 09, 2007, Hashem Taha wrote:
>
> i am trying to do MD simulation on a monosaccharide in TIP4P water. I
> have tried the simulation with TIP3P and it worked perfectly. Using
> the same input files but with TIP4P did not work because of the
> nonbonded cutoff of 8 angstroms.

What do you mean by the "same input files"? Maybe you should post the
commands you gave to LEaP: it is unfortunately easy to make mistakes in
setting up non-default water models.

Also, what is it that led to you think the problem involved the non-bonded
cutoff? Changing that to a smaller value is probably not a good idea. I
would guess that you still need to find to real origin of your problems.

....dac

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