[AMBER] RMSD discontinuity between NPT and NVT with restraints

From: Thomas Gaillard <thomas.gaillard.polytechnique.edu>
Date: Wed, 6 May 2020 17:57:00 +0200

Dear Amber developers and users,

I have an equilibration protocol with an NPT phase followed by an NVT
one. The pressure control is ntp=1, the temperature control ntt=3. The
same restraints are applied in the two phases (with the group syntax),
the reference coordinates for the restraints are always the same (the
initial structure, passed with "-ref" in inpcrd format, as written by
Leap with saveamberparm). The restart files are in netcdf restart format
(ntxo=2). I am using pmemd.cuda with Amber 14.

I observe a structural discontinuity at the beginning of the NVT phase,
corresponding to a contraction of the RMSD with respect to the reference
structure. It looks as if the structure was brutally brought back to the
reference when the NVT phase begins.

A possible interpretation would be that during NPT, the reference
structure is scaled at the same time as the simulated structure when the
box dimensions change. This scaling of the reference structure would
then be lost when the NVT phase begins as it is reread from the inpcrd.

Is this interpretation correct? Is there a way to perform NPT then NVT
with restraints that would prevent the discontinuity problem that I

I hope that my explanation is clear enough, I can provide additional
informations if needed.

Thank you for your time,

Thomas Gaillard
Professeur assistant
Laboratoire de Biochimie
Ecole Polytechnique
91128 Palaiseau cedex
tel: +33 1 69 33 48 62
fax: +33 1 69 33 49 09
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Received on Wed May 06 2020 - 09:00:02 PDT
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