AMBER Archive (2009)

Subject: [AMBER] explicit solvent NMR refinement

From: Sally Pias (sallypias_at_gmail.com)
Date: Sun Jun 28 2009 - 03:46:56 CDT

Hello all,

I am following a protocol for explicit solvent refinement of NMR
structures described by Xia, et al. (J Biomol NMR, 22: 317–311, 2002).
 The protocol uses Berendson temperature control throughout, with a
heat bath coupling constant of 1.0 ps. My understanding from reading
Amber Reflector Archive discussions is that Langevin temperature
control is now preferred in general, particularly when one is
interested in dynamics. Does this preference apply to NMR refinement,
where it is not really dynamics that one is after? Is it appropriate
to modify the protocol to use a Langevin thermostat? If so, what
collision frequency would be suitable?

I have outlined the protocol below.

Thank you for any guidance,

Sally Pias

=======
Refinement protocol, following Xia et al. (2002):

1) Gradual heating:
       3 cycles of 40 ps (0-50 K, 50-100 K, 100-300 K)
       Constant volume
       5 kcal/mol*A^2 restraints on protein
       TAUTP=1.0
       TAUP=0.2 (perhaps a mistake, as this is a constant volume simulation)

2) Constant pressure MD at 300 K with weak harmonic restraints
       2 cycles of 40 ps (TAUP=0.2, then TAUP=1.0)
       5 kcal/mol*A^2 restraints on protein

3) Constant volume MD at 300 K with weak harmonic restraints
       1 cycle of 40 ps with 5 kcal/mol*A^2 restraints on protein
       1 cycle of 60 ps with 0.5 kcal/mol*A^2 restraints on protein
       TAUTP=1.0
       TAUP=1.0 (perhaps a mistake, as this is a constant volume simulation)
       Time step 2 fs

4) Constant volume MD at 300 K without harmonic restraints
       100 ps, with time step 1 fs
       TAUTP=1.0
=======

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