Has anyone met this problem?
I use Amber 11 (pmemd.MPI and pmemd.cuda) with all latest bugfixes applied
(!), the bug doesn't appear if no restraints are used in simulations.
2011/1/30 Dmitry Mukha <dvmukha.gmail.com>
> Dear Amber users,
>
> is there any opportunity to run MD of NPT ensemble with harmonic
> restraints? I have tested many combinations of taup, vrand (ntt=2),
> gamma_ln(ntt=3), restraints_wt, and all that I've got are systems with
> density equal or below starting value. Generally, systems blow up due to the
> energy, I guess, introduced by barostat action on restrained atoms. These
> atoms work as springs releasing additional potential energy after coordinate
> scaling. Temperature raises continually, and barostat scales coordinates in
> order to enlarge system's volume and, thus, compensate growing pressure. If
> dt is small enough, this process can be computed till almost stable state
> with density significantly below initial. Final density values depend on
> termostat coupling tightness. With tight coupling (low vrand or high
> gamma_ln) systems do not evolve and density remains almost the same as
> initial. How to overcome these problems and equilibrate density with
> restraints applied to solute atoms?
>
> --
> Sincerely,
> Dmitry Mukha
> Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
>
--
Sincerely,
Dmitry Mukha
Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
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Received on Mon Jan 31 2011 - 08:00:04 PST
