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
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Received on Sat Feb 20 2021 - 16:30:02 PST
