AMBER: separate thermostats for different molecules

From: Arvid Soederhaell <>
Date: Mon, 4 Aug 2003 15:13:11 +0200 (MEDT)

Dear All

I wonder if it is possible to use separate thermostats for different parts
of a simulation? I have a membrane simulation that runs relatively nice,
but I have the impression that the lipids are much colder than the
surrounding water. I have not actually measured the temperature in the
different parts of the box, but the lipids are terribly well ordered and
it looks like gel phase, rather than liquid crystaline phase.

I have read (Tieleman (1999) Biophys. J. 76:40-9) that one should use
separate thermal baths for the water and the lipids, to avoid
temperature gradients. I believe that I have such an undesired temperature

In sander 5 there was a command "ISOLVP" that seems to be useful for
this, but I need to use sander 7 because of Ewald and anisotropic scaling
of pressure.


    Arvid Soderhall

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Received on Mon Aug 04 2003 - 14:53:02 PDT
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