Dear Anthony,
> I have a question, for example if I want to run a 3ns
> simulation and I set the
> tempi=0.0 and temp0=300 how much time of the 3ns will be use
> for system
> equilibration??? Is preferable to equilibrate the temperature
> of the system
> with restrain???
In the example you give it would get to 300K very quickly. Roughly in line
with the value of tautp (ntt=1) or in relation to the size of gamma_ln
(ntt=3). Typically this will be within 5 or 10ps or so.
Ideally if your system is quite large and explicit solvent it is advisable
to heat slowly using weight restraints. E.g.
ntt=1,dt=0.002, nmropt=1,
/
&wt type='TEMP0', istep1=0,istep2=100000,
value1=0.1, value2=300.0, /
&wt type='END' /
This will heat the system linearly from 0.1K to 300K over 200ps.
I hope this helps
All the best
Ross
/\
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
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Received on Mon Aug 29 2005 - 16:53:00 PDT
