Subject: CHARMM: Is there any problem with velocity Verlet in c28b2 ?

From: Andrij Baumketner <[email-masked]>
Date: Mon, 16 Sep 2002 19:38:48 -0700 (PDT)

Dear CCLers,

I am trying to simulate a short peptide fully solvated in TIP3 water by 
using 28beta2 version of CHARMM. I intend to employ constant NVT 
conditions and, although the system under study is not particularly large, 
I need a parallel implementation of the code. As far as I understand, in 
CHARMM the NVT ensemble can only be generated in parallel by using 
velocity version (VVER key) of the Verlet algorithm combined with the 
Nose-Hoover thermostat. (I could probably use CPT but I'm not sure about 
how scaling of coordinates is dealt with there). When running a short 
simulation on a fully equilibrated system I find that:

a) VVER version produces considerably lower potential energy than the 
original Verlet (non-parallel) algorithm when the SHAKE is applied. The 
non-parallel Verlet gives results consistent with the CPT ensemble 
simulations.

b) if SHAKE is not applied the VVER algorithm just goes unstable. It 
pumps all the energy into vibrations of both solute and solvent molecules 
until the algorithm breaks. The original Verlet works just fine under the 
same conditions.

I would appreciate any comments or suggestions from those who have 
encounter these problems before.

With best wishes,

Andrij 

-- 
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A. Baumketner
Postdoctoral Fellow
Department  of Chemistry and Biochemistry 
University of California at Santa Barbara
Santa Barbara, CA 93106, USA
Tel: +1-805-252-2611
Fax: +1-805-893-4120
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