AMBER Archive (2009)

Subject: Re: [AMBER] vlimit in TI with soft core potential

Date: Wed Jun 17 2009 - 03:47:38 CDT

Dear MEI,

> BTN, recharging biotin. But the free energy changes in the first and the
> third steps are very large. But we only care about their difference,
> which is relatively small. I think this process will bring large errors
> into the final result. So I want to try a 2-step way, in which the
> charges of IMI change to those of BTN and then the vdw parameters. The

The 1st and 3rd step dvdl can be very large if e.g. 1-4 interactions are
removed. That does not necessarily mean the corresponding result is
inaccurate. The electrostatic results are normally well converged,
especially the part stemming from 1-4-EE and the large free energy changes
should cancel out well.

If you have charges left on some softcore atoms in step 2 of your 2-step
process, the simulation will probably crash at some lambda point, as soon
as the vdw is softened enough for a solvent atom to crash into the exposed
charge. That is the reason why the 3-step process is necessary for now. We
are working on a better way to do TI in less steps, but it will have to
wait for Amber11...

Kind Regards,


Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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