Yes, these systems are identical w.r.t. #protein, water and cofactor atoms
only charges on cofactor are different.
On Mon, Feb 22, 2021 at 5:18 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I'm still not sure what you're doing exactly, and the details might matter.
> Are these identical systems? Same # wat etc? Comparing the absolute
> energies will be difficult if the systems differ, since the zero for energy
> is arbitrary in MM.
>
> On Mon, Feb 22, 2021, 5:37 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
>
> > 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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> > > > >
> > > > >
> > > > > --
> > > > >
> > > > > 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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>
--
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 - 04:00:02 PST
