RE: AMBER: Fluctuation in temperature

From: Ross Walker <>
Date: Thu, 4 Nov 2004 12:05:57 -0800

Dear Anshul

The Generalised Born code is very fast for small systems but as system size
increases it's performance drops off rapidly. Thus you may find that you
could actually run your system in explicit solvent with periodic boundaries
faster than you can run it in implicit solvent. Try solvating the system in
a truncated octahedral box of TIP3P water and see how it runs. I would try
and stay away from gas phase (non GB) calculations as such simulations are
good representations of reality and you are likely to have problems with
stability etc even with large cutoffs.

As for increasing the efficiency of GB this would require quite a bit of
modification to the Gerneralised Born routines. This is something that will
be investigated at some point but is likely to take a while.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

> -----Original Message-----
> From:
> [] On Behalf Of
> Sent: 04 November 2004 14:10
> To: amber mail reflector
> Subject: AMBER: Fluctuation in temperature
> 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

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Received on Thu Nov 04 2004 - 20:53:00 PST
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