AMBER Archive (2006)

Subject: Re: AMBER: md and implicit solvation

From: Adrian Roitberg (
Date: Tue Oct 24 2006 - 19:19:34 CDT

Jardas sucuriba wrote:
> Hi all
> I ran 50 ps of an MD simulation (equilibration phase) using implicit
> solvation. However my calculation took 3 days to complete! Is it normal
> to take so long? I am really worried because I want to run a production
> phase of 1 ns. I wonder if someone could tell me if there is something
> wrong with my script or pehaps suggest me modifications to improve it.
> My system has around 15000 atoms.
> &cntrl
> imin=0, ntx=1,
> dt=0.002, nstlim=25000, igb=5,
> ntpr=100, ntwr=100, ntwx=100, nrespa=2,
> ntb=0, scee=1.2, cut=16.0,
> ibelly=0, ntt=3, gamma_ln=1.0, ntc=2, ntf=2,
> temp0=300.0, tempi=300.0, tol=0.000001,
> /

Without sounding condescending:

Of course it is normal with a very slow computer, not too many nodes in
parallel, a bad compilation, a large protein, etc etc.

So as usual we ask people that ask questions to the list:

Give us the details on the system please and we might be able to help !


                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida PHONE 352 392-6972 P.O. Box 118435 FAX 352 392-8722 Gainesville, FL 32611-8435 Email ============================================================================

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