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
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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 - 11:53:00 PST
