Dear Carlos, David and All,
The E-difference between two states (1 and 2) is 21 kcal/mol under
non-periodic and 26 kcal/mol under periodic conditions.
This means that the variation in differences of Es between the two states
is about 5 kcal/mol when we change how the SP Es are calculated (periodic
vs non-periodic system).
But as you might have guessed, there is a huge difference in the speed of
these calculations.
The calculation for the periodic system with cut=9 finishes within 10
minutes while for non-periodic with cut=9999 takes 4-6 hours depending on
the size of the system (2000 snapshots were analyzed).
Now I'm investigating how this E-diff between two states changes with
respect to many factors e.g. box size, force field, mutation of key
residues etc.
Thus can you please suggest which system (periodic or non-periodic) might
be considered more reliable (if at all) to dwell more deeply into the
effect of factors mentioned above?
Or one has to calculate all and then analyze how it relates to the
experimental data?
Looking forward to your insightful suggestions and tips for doing this
analysis.
Thank you and best regards.
On Sun, Feb 21, 2021 at 5:38 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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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> > >> > >
> > >> > _______________________________________________
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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,
> > > ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> > > 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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>
--
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 Mon Feb 22 2021 - 03:00:02 PST
