AMBER Archive (2004)

Subject: Re: AMBER: Fluctuation in temperature

From: Oliver Hucke (
Date: Thu Nov 04 2004 - 12:14:36 CST


I am surprised by the speed of your GB simulation. Did you try a
simulation with explicit solvent? What hardware are you using?
I have a system that might be of comparable size to yours (536 amino
acids). I am using a truncated octahedral box with altogether ~50000
atoms and get 75ps/day on a double processor linux box (Intel Xeon
2.4GHz). I would be reluctant to use distance dependent dielectric for
serious simulation work.

Oliver wrote:
> Dear amber users, I am doing dynamics studies on a protien molecule. The
> system I am working on is quite large (597 residues and 9726 atoms). To
> neutralise it I have added 33 IB atoms. Previously I started with dynamics
> using GB model, but it was taking quite long to do the job (approximately
> 3 hrs per ps). This means it would have taken more than 2 months to
> complete just 500 ps of dynamics.
> To reduce it I tried to do dynamics using distance dependent dielectric
> (eedmeth=5 and dielc=4), with this the speed is fine I am facing other
> problems. after minimization, I was raising the temperature from 0K to
> 300K in small steps (30K per 10ps). What I observed was that during the
> run the IB molecules are drifting away and thus I got the following error:
> The system has extended beyond
> the extent of virtual box.
> Which I think is due to the movement of IB atoms. To overcome this I tried
> to put restraints on the IB atoms with a force constant of 3. Now the
> temperature of the system started to rise rapidly and within .7ps it rose
> to about 60K and then it started to decrease. the temperature then
> decreased to 1K and then again started to increase. This cycle of increase
> till ~60K and then decrease continued.
> Next I reduced the force constant to 1. Now the temperature did not rise
> till 60K but the behaviour was same ie it rised till 27K and then
> decreased till 1K and then agian rise.
> The run with Gb model was running smoothly but then there was the factor
> of time. Can anyone explain this behaviour. Any suggestion regarding how
> one can increase tyhe speed using the GB model will also be helpful.
> the oputput which I got is attached with this mail
> -------------------------------------------------------
> Thanks in advance for your valuable suggestions and advises.
> With best regards,
> Anshul Awasthi
> Bioinformatics Center
> Institute of Microbial Technology
> Chandigarh, India.
> Mobile +91-9872220352
> ------------------------------------------------------------------------

Oliver Hucke, Dr.
Biomolecular Structure Center Health Sciences Building - K418C
Dept. of Biochemistry 1959 NE Pacific St.
University of Washington phone: (206) 685 7046
Box 357742 fax : (206) 685 7002
Seattle, WA 98195-7742 email:

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