AMBER Archive (2007)

Subject: Re: AMBER: Error when doing a TI simulation: "vlimit exceeded

From: ming hui (yongminghui_at_gmail.com)
Date: Thu Nov 15 2007 - 18:48:05 CST

Dear Thomas,
Yes I am removing all electrostatic interactions before removing vdW
interactions, the problem I am facing begins right at the start in the first
stage when only electrostatic interactions are disappearing, sorry I forgot
to mention this.

However, for the case of a TIP3 water molecule, the hydrogen atoms are
already 'soft atoms' with non zero charges I suppose? Since the nonbonded LJ
parameters are already zero from the start. But I have already simulated the
system for about 10 ns before using the end coordinates as the starting one
for my TI without any such reported errors.

One difficulty I had in setting up the perturbed prmtop files for this TI
was: in the simulation i just mentioned, the water molecule that mediated
interactions between Tris and the protein had come from the surrounding bulk
solvent; it was not a crystallographic water i.e. not in the starting PDB
file. I could not use the pdb file specifying the final state of the system
in the first simulation as the prmtop file created would not reflect that a
rectangular box for PBC existed, or the dimensions of that box. So I had to
start with only the protein structure, resolvate my box, then to locate the
water molecule corresponding to the one of interest in my restart file, i
just used >"select mol.6280" in xleap and edited the parameters of the
selected molecule etc. I'm not sure if this would cause any problems though.

Thank you so much for your response, I really appreciate it.

Regards,
Ming Hui

On 11/16/07, Thomas Steinbrecher <steinbrt_at_scripps.edu> wrote:
>
> Hi Ming,
>
> I am not sure this is the source of your problems, but TI calculations
> normally should be broken down into two steps and from what you write, Im
> not sure if you do that.
>
> First remove the partial charges on all atoms that are about to
> diappear, then in a second separate simulation remove the chargeless
> atoms. Otherwise you will have, especially at high lambdas, nonzero
> charges on very soft atoms, which could mean another atom gets close to
> them and feels a huge force, resulting precisely in the vlimit error you
> mention.
>
> Try out to break down your calculation into two steps by making a prmtop
> file with all atoms still there, but zero partial charges on the ones that
> will disappear, then use this as your end point of the first and starting
> point of the second simulation.
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> San Diego CA 92037, USA
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