Re: AMBER: md and implicit solvation

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Tue, 24 Oct 2006 20:19:34 -0400

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 !

Adrian

-- 
                            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 adrian.qtp.ufl.edu
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Received on Wed Oct 25 2006 - 06:07:29 PDT