Dear David and All,
I'm already using Daniel Roe's AmberMDPrep script (coupled to github
version of cpptraj) to equilibrate the water density.
Your suggestion on using the closest command in interesting, I will try
that option next time on other systems.
For e.g setup MD for waterbox 30A, do MD, then use closest to trim at
different sizes (probably from the center of the box/protein?) and then
estimate the SP Es.
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?
If I chose ntb=2 and run sander.MPI jobs can I expect to get SP Es in
periodic systems (as Carlos suggested to try out)?
Are these likely to be more meaningful when I take *relative differences*
between two systems with the same atom type/numbers but different charges?
Thanks a lot for your valuable suggestions and expert comments.
Best regards
On Sat, Feb 20, 2021 at 7:46 PM David A Case <david.case.rutgers.edu> wrote:
> On Sat, Feb 20, 2021, Vaibhav Dixit wrote:
>
> >I ran MD with 10, 15 and 30A TIP3PBOX to understand the effect of box size
> >on relative FF energies between two systems.
> >The calculations when well with 10 and 15A box size.
> >But I'm getting the following error in mdout file with the system setup
> >with 30A TIP3PBOX.
>
> It looks like you set up tleap for a periodic system, but then set ntb=0
> in your MD input. But it's not clear what you are trying to compute here:
> do you just want a single-point energy as a function of amount of solvent?
>
> Also, remember that tleap's solvate options only create a starting point
> for
> further simulation. For example, the starting density is far from 1.0.
>
> Here's one idea, if I am reading your intent correctly: run a periodic
> simulation in the usual way, and get each system equilibrated to its final
> temperature and density. Then use the "closest" command in cpptraj to
> get various sizes of water box. For each of these, do a non-periodic
> calculations (cpptraj can help you get the prmtop files), and use igb=6
> to carry out the single point calculations.
>
> ...good luck...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
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Received on Sat Feb 20 2021 - 07:00:05 PST
