Thanks InSuk! The NPT equilibration appears to be working fine now;
that mistake was undoubtedly a leftover from the uncharging script.
As far as I can tell though, there was no error message and the
simulation definitely didn't stop. Nevertheless, I think I will file
this episode under "failures of search and replace (and my eyes)"...
Paul
On May 18, 2010, at 6:48 PM, InSuk Joung wrote:
> 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 - 19:30:03 PDT
