Dear Thomas,
actually, I'm using Amber 8, is it a bad thing?
Regards,
Ming Hui
On 11/16/07, Thomas Steinbrecher <steinbrt.scripps.edu> wrote:
>
> Hi Ming,
>
> take a look in where your two prmtop files differ (I assume that you use
> Amber9 for TI), just to check if really only the charges are different
> between V0 and V1. Also, just to make sure, are your input coordinate
> files absolutely identical for both processes?
>
> You can also try to run a short simulation with ntwx=1 right were your
> jobs crash to see if any atoms behave strangely.
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> San Diego CA 92037, USA
>
> On Fri, 16 Nov 2007, ming hui wrote:
>
> > 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.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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> >
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Received on Sun Nov 18 2007 - 06:07:37 PST
