It looks ok as long as all of the terms related to energy match the MD run.
On Sun, Feb 21, 2021, 1:58 AM Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
> Dear David, Carlos and All,
> The following combination of options for running SP FF E estimation is
> working for periodic system options.
> Can you please take a look and let me know if this looks OK?
> ntb=2 is not compatible with imin=5, thus I have chosen ntb=1 assuming that
> since these are SP FF E calculations it doesn't matter if one chooses
> constant volume or pressure because the atoms are not going to move anyway.
> Nonetheless, I might have accidentally chosen a keyword combination that is
> not physically meaningful (about which Amber is not a warning), thus
> need your assessment on the same.
> thank you and best regards
>
> &cntrl
> ntx=1, ntpr=1, ntwx=1,
> imin=5, maxcyc=1, !Single-point energy calculation on each frame
> ntb=1, ntp=0, ntc=2, !periodic
> cut=9,
> /
>
> On Sun, Feb 21, 2021 at 9:26 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
>
> > My sander input file is very similar to that given at the bottom of page
> > 134 of Amber20 manual and is the following.
> > Please suggest what modifications should be made to this.
> > Should I use igb=6 instead of the cut option (as suggested by David)?
> >
> > &cntrl
> > ntx=1, ntpr=1, ntwx=1,
> > imin=5, maxcyc=1, !Single-point energy calculation on each frame
> > ntb=0, !Non-periodic
> > cut=9999., !Calculate all solute-solute interactions
> > /
> >
> >
> > On Sun, Feb 21, 2021 at 5:26 AM Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> >> If you did the MD with periodic system, you should evaluate the energy
> for
> >> ap the same way. Otherwise it won't be the energies for the conditions
> you
> >> simulated. I suggest using a similar I out as for md, and look at the
> imin
> >> flag in sander, specifically the imin=5 option. That is what I would do.
> >>
> >> On Sat, Feb 20, 2021, 6:32 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
> >> wrote:
> >>
> >> > Sorry if my description wasn't confusing. I did MD with periodic and
> sp
> >> > calculations with nonperiodic system.
> >> > Thanks for suggesting, I will try that out.
> >> >
> >> > On Sun, Feb 21, 2021, 03:40 David A Case <david.case.rutgers.edu>
> >> wrote:
> >> >
> >> > > On Sat, Feb 20, 2021, Vaibhav Dixit wrote:
> >> > > >
> >> > > >Now I already have MD and SP (nonperiodic) Es for systems with
> >> waterbox
> >> > > >sizes 10, 15 and 25A (thus I'm guessing closest in not required
> now).
> >> > Can
> >> > > >you please suggest, what are probable reasons for the original
> MAXPR
> >> > error
> >> > > >and how to try to fix it?
> >> > >
> >> > > You can try to set igb=6. But I'm not sure how you did your MD on
> the
> >> > > nonperiodic systems. If you sure that you have a good water
> >> environment,
> >> > > then using igb=6 may help.
> >> > >
> >> > > ....dac
> >> > >
> >> > >
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> >
> >
> > --
> >
> > Regards,
> >
> > Dr. Vaibhav A. Dixit,
> >
> > Visiting Scientist at the Manchester Institute of Biotechnology (MIB),
> The
> > University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> > AND
> > Assistant Professor,
> > Department of Pharmacy,
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> > Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> > VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> > India.
> > Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> > Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> > https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> >
> > ORCID ID: https://orcid.org/0000-0003-4015-2941
> >
> > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >
> > P Please consider the environment before printing this e-mail
> >
> >
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> P Please consider the environment before printing this e-mail
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Received on Sun Feb 21 2021 - 04:30:02 PST
