[gmx-users] Free energy calculations with pull code and umbrella sampling

Kortzak, Daniel d.kortzak at fz-juelich.de
Mon Feb 9 09:50:49 CET 2015

Hi All,

I have one quick questions about free energy calculations via pull code+umbrella sampling. (see below for some further information on what I am trying)
First of all I think Justin is right umbrella sampling is much more straightforward. In particular in my situation where I see spontaneous binding at the site I am interested in, i.e. I already have a pathway of the ion to the binding site.
So what I would do now is: Skip the pull code and just use the pathway I already have for the umbrella sampling. Again my question is: Is this sensible?
Of course I have to check if the spacing of the pathway is close enough (output frequency of the xtc was 10ps) but on first sight I think it is, I could easily construct ~30 intermediates from the data I already have.
If I need more intermediates my approach would be to use frames I already have and only pull between the positions of those frames instead of pulling the whole way from the binding site to the bulk.

>>On 2/5/15 6:59 AM, Kortzak, Daniel wrote:
>> Dear All,
>> I want to calculate the free energy of binding of a single sodium ion to a protein. I want to do this by decoupling the ion in the binding site (with the couple-moltype approach). The work-flow I have in mind is roughly:
>> 1. Start with ion in binding site
>> 2. Turn on position restraints (since this only one atom I don't have to care about orientation etc.)
>> 3. Decouple
>> (And do the same for a ion in bulk solution in another simulation.)
>> First of all is this sensible or are there better ways of doing this?
>Wouldn't just using the pull code to do umbrella sampling be a much more
>straightforward approach?  You don't have to deal with compensating for
>artifacts associated with the restraint potential during decoupling and removing
>a charge from the system.

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