AMBER Archive (2006)

Subject: Re: AMBER: md and implicit solvation

From: Jardas sucuriba (
Date: Tue Oct 24 2006 - 20:29:35 CDT

My system is SuSE Linux 9.2 (x86-64) and I used two nodes.
What I thought strange is that running the 50 ps in explicit solvation
(using the same protein and 2 nodes) takes only half a day. Is it normal
this difference between the two types of MD? As I cannot use more than two
nodes is there other way to "speed up" the simulation?


>From: Adrian Roitberg <>
>Subject: Re: AMBER: md and implicit solvation
>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 !
> 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
>To announce that there must be no criticism of the president,
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> -- Theodore Roosevelt
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