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
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>
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>
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>
> 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 Sat Feb 20 2021 - 23:00:02 PST
