AMBER Archive (2005)

Subject: Re: AMBER: Temperature equilibration

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Mon Aug 29 2005 - 14:47:36 CDT

Thank you for your answer Ross.

Is possible to do this to set the start temperature of the replicas in a
replica exchange simulation?

Best regards
Anthony
 
On Monday 29 August 2005 9:44 am, Ross Walker wrote:
> 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
>
>
>
> /\
> \/
>
> |\oss Walker
> |
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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>

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