AMBER Archive (2006)

Subject: AMBER: Question regarding lastrst and taup

From: Priti Hansia (priti_at_mbu.iisc.ernet.in)
Date: Wed Oct 25 2006 - 01:37:09 CDT

Dear Amber users,

I have a basic question regarding lastrst and taup values. I have done two
simulations on the same protein at a high temperature (600K) for only
500ps. The box size of the two simulations are different (8 and 12
Angstrom respectively) and all the other initial conditions were same. But
the simulations had stopped saying that I should increase lastrst. So in
the first simulation I increased the lastrst value to 5000000 and changed
taup value to 2.0 whereas in the other simulation I kept the taup value
1.5 and had to change the lastrst value to 15000000 as suggested by the
error. Now when I check the RMSd values, in the first simulation it
reaches around 8 Angstrom and in the second one its around 15 Angstrom
after 500ps of simulation ! Is this kind of different result expected with
just different box size and different values of taup and lastrst ? My
protein after 500ps of first simulation is quite intact whereas in the
second one its very much distortd !

Any suggestion would be of great help.

Thank you,

-Priti

Priti Hansia
Prof. Saraswathi Vishveshwara's Lab
Molecular Biophysics Unit
Indian Institute of Science
Bangalore - 560012
India
Tel: 91-80-22932611
Fax: 91-80-23600535

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