[gmx-users] Re: Re: Re: Re: Size of perturbed groups in FEP

Bruce Milne bfmilne at ff.up.pt
Wed Jan 18 13:21:12 CET 2006

Hi David,

I saw your communications with Maik. Can you suggest any literature that 
would be a good background reading for this particular area? e.g. the 
stuff you mentioned below suggesting that hysteresis might be a 
significant problem in this type of simulation.



gmx-users-request at gromacs.org wrote:

>About the rate of change... I recommend *not* doing time-dependent
>calculations. See my exchange with Maik Goette on this subject on here just
>a few minutes  ago. The literature suggests these tend to be pretty
>hysteretic. Instead, run simulations at specific lambda values where lambda
>modulates between your original system and your final system. Then you can
>do error analysis at each of these lambda values to try and get an estimate
>of how long you need to run (i.e. how long to extend your simulations by) to
>get within the error you want. Probably a good starting length is >1ns at
>each lambda value (after equilibration).
Dr. Bruce F. Milne PhD
Faculdade de Farmácia
Universidade do Porto
Rua Aníbal Cunha - 164

email: bfmilne at ff.up.pt
CEQOFFUP: http://www.ff.up.pt/ceqoffup/ceqoffup.html
Faculdade de Farmácia: http://sigarra.up.pt/ffup/web_page.inicial

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