Hello Vinicius
finddgref.py -mdexec $AMBERHOME/bin/sander -i finddg.in -p nhp2.prmtop -c
equil.rst -cpin nhp2.cpin -log finddg.log
I start with a equilibrated system ( minimized, heated, and equilibrated
with NPT, igb=2) . Also I tried the option -dgrefest
Santo
On Mon, 20 Jan 2020 at 15:16, Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>
wrote:
> Hello Kolattukudy,
>
> There are some optional flags in finddgref.py that should help you with
> that. May you copy the exact command you are using and the output
> finddgref.py is printing so I can give you a suggestion?
>
> Thanks,
>
>
> VinÃcius Wilian D Cruzeiro
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633<tel:+1(352)846-1633>
>
> On Jan 20, 2020, at 10:44 AM, Kolattukudy P. Santo <
> santotheophys.gmail.com<mailto:santotheophys.gmail.com>> wrote:
>
> [External Email]
>
> Hi
> I am trying to run cpHMD for a non-standard molecule. I find it hard for
> finddgref.py to converge and the fraction of protonation % is very
> fluctuating (1 million equillibration steps) . My residue is pretty large
> ( about 120 atoms ) as it is a side chain of a carbohydrate polymer
> Any strategy for fast convergence ?
>
> --
> *Dr. Kolattukudy P. Santo*
> *Post doctoral Associate *
> *Department of Chemical and Biochemical Engineering*
> *Rutgers, The State University of New Jersey*
> *New Brunswick, New jersey*
> *USA*
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--
*Dr. Kolattukudy P. Santo*
*Post doctoral Associate *
*Department of Chemical and Biochemical Engineering*
*Rutgers, The State University of New Jersey*
*New Brunswick, New jersey*
*USA*
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Received on Mon Jan 20 2020 - 13:00:02 PST
