Dmitri,
Many thanks for the comprehensive and very helpful reply.
My very best wishes
George
On Mar 13, 2012, at 9:15 PM, Dmitry Mukha wrote:
> Ok, if x is a number of snapshots sufficient to get convergence for energy
> of binding for system 1 and y is similar parameter for system 2, and x is
> larger than y, you will be lucky to find an algorithm to make an estimation
> of such a numbers in automatic fashion. Probably, you should take the
> largest number of snapshots, x, multiplied on some coefficient larger than
> 1. Then, you can run your script for MMPBSA analysis for a set of your
> compounds being sure that production run length won't be the reason of
> wrong results. So, take as much as you can ))) (that is what I mean), both
> for equilibration and for production. The reason for the largest error
> still hides in wrong coordinates for protein-ligand complex, ff
> parameterization and so on. The former can be overcome by long
> equilibration if energy barriers are not too high.
>
> 2012/3/13 George Tzotzos <gtzotzos.me.com>
>
>> Dear Dmitri,
>>
>> Many thanks for this. It makes sense to me, except for the last part
>> "larger than optimal for individual case". What do you mean by this
>> (individual case).
>>
>> Best regards
>>
>> George
>>
>> On Mar 13, 2012, at 8:19 PM, Dmitry Mukha wrote:
>>
>>
>>
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>>
>
>
> --
> Sincerely,
> Dmitry Mukha
> Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
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Received on Tue Mar 13 2012 - 14:00:03 PDT
