See your mdin_vdw_equi_v1_l1
It should be 'ifsc=1', right?
I think an error should stop the run when ifsc are different at the
two input files. If not, it would be good to have a check routine in
the code to prevent this kind of mistakes.
On Tue, May 18, 2010 at 9:24 PM, Paul S. Nerenberg <psn.berkeley.edu> wrote:
> Hi all,
>
> As a prelude to parameterizing some ions, I am trying to calculate the
> solvation free energy of K+ (potassium) using the various TI bits in sander.
> I have no problem "uncharging" potassium from +1 to 0 -- everything works
> fine and I get what seems to be a very reasonable deltaG for this step
> (~72.6 kcal/mol). When I use the softcore potential facility to make the
> neutral potassium atom turn into nothing (i.e., disappear), however, I run
> into a weird problem...
>
> My initial minimization and NVT heating steps finish fine and I don't see
> anything out of the ordinary in the output or restart files for those parts.
> However, when I try to perform an NPT/density equilibration, the simulation
> hang just after reading the restart coordinates/before starting dynamics
> without dying or giving any sort of error (see link below). I was careful
> to be sure that the \lambda=0 system was the neutral potassium + water box
> and that the \lambda=1 system was just the water box (and that these were
> properly generated by tleap). Likewise, I put the potassium atom in the
> scmask for \lambda=0 system and left the scmask for the \lambda=1 system
> blank. Overall I think that the system setup is OK, so I'm at a bit of a
> loss to figure out where to start the troubleshooting.
>
> In the hopes that someone might spot something obvious, I've posted all my
> files to: http://www.ocf.berkeley.edu/~psn/potassium/<http://www.ocf.berkeley.edu/%7Epsn/potassium/> The naming convention is pretty simple -- K0_wat is for the \lambda=0
> system, K0_watonly is for the \lambda=1 system. All the mdin scripts, group
> files, etc. are generated by the bash script setup_vdw.sh (currently set to
> generate scripts just for one lambda value). The last written output of the
> NPT equilibration is here:
> http://www.ocf.berkeley.edu/~psn/potassium/output/K0_wat_vdw_equi_v0_l1.out<http://www.ocf.berkeley.edu/%7Epsn/potassium/output/K0_wat_vdw_equi_v0_l1.out>
>
> Many thanks in advance,
>
> Paul
>
> P.S. If all else fails, I realize that I could go the dummy atom route and
> probably use the "old" (i.e., non-softcore) TI routines without issue, but I
> figured it was worth trying to fix this first.
>
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>
--
Best,
InSuk Joung
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Received on Tue May 18 2010 - 19:00:03 PDT
