maxcyc is an option in the &nmode namelist in your MMPBSA.py input file. The
default value is 10000.
-Bill
On Tue, May 31, 2011 at 12:06 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
> Thanks for reply
> Actually I have 2ns trajectroy and I am doing MMPBSA nomde in parts.
>
> For 1-500ps it gave warning
> WARNINGS:
> Not all of your snapshots minimized within tolerable limits for nmode
>
>
> But for 501-1000ns didnt gave any warning
>
> DELTA S total= -54.4966 +/- 25.8445 (for 1-500ps)
>
> DELTA S total= -53.9573 +/- 19.4499 (for 501-1000ps)
>
> So I think It may me memmory issue.
>
> As you have suggested to increase maxcyc but I am using MMPBSA.py so how I
> can
> increase
> maxcyc?
>
> > I would say that despite you actually getting entropy results in the
> output
> > file, I would not put a lot of stock into the reliability of those
> results
> > if some of the snapshots did not properly minimize. I would suggest
> > increasing the maxcyc in the input file to improve your chances of
> > successfully minimizing all your snapshots.
> >
> > -Bill
> >
> > On Sat, May 28, 2011 at 12:45 PM, Sangita Kachhap <sangita.imtech.res.in
> >wrote:
> >
> >> Thanks for reply
> >>
> >> I have got entropic result this warning is written at the end of output
> >> file.
> >>
> >> Here I am attaching energy output file.
> >>
> >>
> >> > My guess is since you got this warning message that you did not get
> any
> >> > entropic results with your calculation, is that correct? In that case,
> >> you
> >> > will need to fix this problem in order to get your final results.
> >> >
> >> > -Bill
> >> >
> >> > On Sat, May 28, 2011 at 5:41 AM, Sangita Kachhap <
> sangita.imtech.res.in
> >> >wrote:
> >> >
> >> >>
> >> >> Hello All
> >> >>
> >> >> I am doing MMPBSA nmode analysis. Job has completed successfully but
> >> with a
> >> >> warning.
> >> >>
> >> >> WARNINGS:
> >> >> Not all of your snapshots minimized within tolerable limits for nmode
> >> >>
> >> >> Will it affect my final result?
> >> >>
> >> >> With regard
> >> >>
> >> >> Sangita Kachhap
> >> >> JRF
> >> >> BIC,IMTECH
> >> >> CHANDIGARH
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
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> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Bill Miller III
> >> > Quantum Theory Project,
> >> > University of Florida
> >> > Ph.D. Graduate Student
> >> > 352-392-6715
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >> Sangita Kachhap
> >> JRF
> >> BIC,IMTECH
> >> CHANDIGARH
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue May 31 2011 - 09:30:07 PDT
