From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Sat Apr 09 2011 - 01:18:19 CDT
On 8 April 2011 22:48, Ivan Vyalov <VyalovIvan_at_yandex.ru> wrote:
> Well, I took a protein as a common example, but the system is actually cellobiose in ionic liquid. That's why I have these differences and values of free energy don't change with time, so I think it's ok with respect to converrgence. But if I apply bias calculated at the point where the barriers are high, then in point where solute-solvent interactions are switched off my system will be over-biased, won't it?
Apparently, yes. One thing you could do is scale the restraints down,
possibly all the way to zero, as they become less relevant.
> 09.04.11, 00:05, "Jérôme Hénin" <jhenin_at_ifr88.cnrs-mrs.fr>:
>
>> Hi Ivan,
>>
>> On 8 April 2011 21:12, Ivan Vyalov <VyalovIvan_at_yandex.ru> wrote:
>> > Hi Jerome,
>> >
>> > Thanks for reply! So, colvars config should contain lines like these:
>> >
>> > abf {
>> > colvars phi psi
>> > updateBias no
>> > inputPrefix colvarA01o
>> > fullSamples 200
>> > }
>>
>> This looks fine. Setting the fullSamples parameter is a good idea, actually.
>>
>> > And then I start FEP calculations that seems to be working ( I didn't try with solvent yet ).
>> >
>> >
>> > May I ask you one more question?
>> >
>> > If I want to perform annihilation of dipeptide then won't I have to recalculate bias ( along \phi & \psi ) between FEP steps ( perhaps, not between every lambda window )? In my case solvent changes free energy surface quite significantly and if I have barriers ~6 kcal/mol for vacuum then for solvent they are ~16 kcal/mol.
>>
>> Well, you probably don't need the biases to be perfectly accurate,
>> they are just there to improve sampling. It is a bit surprising that
>> solvent effects on conformational free energy are so drastic. Are you
>> confident that the ABF calculations are converged (or close enough)?
>>
>> In principle you can certainly apply different biases at different
>> stages, if you are ready to run more calculations. I am not sure it is
>> worth the effort. It depends on the specifics of your system (and how
>> much time you are willing to spend on it).
>>
>> By the way, an idea just came to my mind: it might be a better idea to
>> replace the data in the gradient file with that in the '.est' file
>> written by abf_integrate. The good thing about that data is that it is
>> a "true gradient" (its curl is zero), whereas the raw data in the
>> '.grad' file is not, due to statistical noise. Applying the bias based
>> on the '.est' file ensures that the biasing force is conservative.
>>
>> Best,
>> Jerome
>>
>>
>> > 06.04.11, 20:45, "Jérôme Hénin" <jhenin_at_ifr88.cnrs-mrs.fr>:
>> >
>> >> Hi Ivan,
>> >>
>> >> That should be possible. Here is how I see it:
>> >> 1) run ABF to get biasing potential
>> >> 2) run FEP with ABF bias, disabling updatePotential to keep the bias
>> >> time-independent.
>> >> In this step, save FEP data and colvars trajectory with the same
>> >> frequency (e.g. 10 timesteps) to make the next step easier
>> >> 3) compute a FEP estimator with unbiased data: you need to reweight
>> >> the ensemble averages based on the applied ABF bias.
>> >>
>> >> Cheers,
>> >> Jerome
>> >>
>> >> On 6 April 2011 11:49, Ivan Vyalov <VyalovIvan_at_yandex.ru> wrote:
>> >> > Hi all,
>> >> >
>> >> > I wonder, is it possible to perform FEP calculations with solute molecule with flattened free energy surface along several reaction coordinates?
>> >> >
>> >> > For instance, if I take dipeptide with conformational degrees of freedom ( dihedrals \phi & \psi ) and two minima defined by them, I should take into account this minima and do something similiar to what is described in JPhysChem 97, 3409.
>> >> >
>> >> > From the other hand I could run ABF, apply forces and perform FEP with flat free energy surface along these coordinates, is it possible in NAMD? Or I should do such task in a different way?
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > with best regards,
>> >> > Ivan
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >
>> > --
>> > with best regards,
>> > Ivan
>> >
>> >
>>
>>
>>
>
> --
> with best regards,
> Ivan
>
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:06 CST