RE: AMBER: question temperature coupling tautp value for RNA

From: Ross Walker <>
Date: Mon, 3 Oct 2005 15:50:47 -0700

Dear Zhuang,

> Hi...I'm simulating RNA in explicit water...I'm just wondering if
> anyone can give me some suggestion on what the value of tautp should
> be...the manual says usually tautp is between 0.5 and 5...with
> default=1...would I be ok using the default value? Otherwise what
> value should I use? thanks

This is really just a tuning parameter for use during heating and
equilibration. Your best bet is just to leave it at the default and see what
happens. If you find that your system has very large deviations from the
target temperature that it take a long time to 'recover' from then you could
try increasing the value of tautp to give greater coupling. On the other
hand if you want the thermostat to have less of an effect on the dynamics of
the system then set the value smaller.

In short, if you don't have a good reason for changing the value leave it at
the default.

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 |

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Received on Mon Oct 03 2005 - 23:53:00 PDT
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