[gmx-developers] sigma6_min?

[hess at sbc.su.se]

> On 2010-09-25 18.55, Shirts, Michael (mrs5pt) wrote:
>> I'm trying to understand some code recently put into nb_free_energy.c
>>
>>              if((c6A>  0)&&  (c12A>  0))
>>               {
>>                   sigma6a      = c12A/c6A;
>>
>>                   if (sigma6a<  sigma6_min)
>>                   {
>>                       sigma6a  = sigma6_min;
>>                   }
>>               }
>>
>>
>> It seems that if sigma6 is changed, then the endstates will not actually
>> correspond to the C12 and C6 parameters specified.  Am I missing
>> something?
>
> This is for the test particle insertion code (Berk correct me if I'm
> wrong...). It will only be used when atoms come very close (which can
> happen when generating coordinates). For normal free energy code one
> would tend to use soft-core I guess.

You're wrong.
I don't know if the sc_sigma minimum issue was discussed on the developers
list before.
The problem is that hydrogen bonding interactions get scaled in
an inconvenient way when hydrogens have small sigma's. Then sigma6
would be large for the oxygen (or nitrogen) and much smaller for H,
which leads to very strong hydrogen bonding at intermediate lambda's.
(note that with separate VdW and Coulomb (de)coupling there are no
such issues)

Berk

>
>
>>
>> Thanks,
>> ~~~~~~~~~~~~
>> Michael Shirts
>> Assistant Professor
>> Department of Chemical Engineering
>> University of Virginia
>> michael.shirts at virginia.edu
>> (434)-243-1821
>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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