Thank you, Dr. Steinbrecher. So I have to give up the 2-step simulation
now. Wish this problem can be solved in the next release of Amber.
Ye
On 6/17/2009, "steinbrt.rci.rutgers.edu" <steinbrt.rci.rutgers.edu>
wrote:
>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,
>
>Thomas
>
>Dr. Thomas Steinbrecher
>BioMaps Institute
>Rutgers University
>610 Taylor Rd.
>Piscataway, NJ 08854
>
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Received on Mon Jul 06 2009 - 09:52:40 PDT
