[gmx-users] free energy calculation and constraint distance?

[bmmothan at ucalgary.ca]

Hello,

What I want to do is calculate the free energy difference of pulling the
ligand away from the receptor. I want to do it using theromdynamic
intergration using the Lamda 0/1 stuff. I am just not clear of the
procedure of how to do it.

I want to constraint several distances between the ligand and the receptor
and then  increase that distance for state B(lamda=1)where the ligand and
receptor are completely separated. For that, I would have to modify my
topology where i define [ constraints ] for the distances i want to
constrain between the ligand and the receptor and input the bond length
for state A(lamda=0) and state B (lamda=1) for each.


will the distances defined move the whole ligand away from the receptor?
since am only defining several distances between ligand and receptor only.

I want to make sure that my procedure above is correct for thermodynamic
integeration.


hope this clearifies what I am trying to say.



Belquis



> Sorry, I really didn't get, what your goal is and what, in fact, you
> really want to do.
>
> For free energy calculations, you can
> - either do Thermodynamic integration (the lambda 0/1 stuff)
> - or pulling (force probe) and afterwards use Jarzynskis theorem
> - or umbrella sampling together with WHAM (if I remember correctly)
>
> Now, it's up to you, which method you favor....may also depend on your
> system/question
>
> Regards
>
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>          mgoette2[at]gwdg.de
> WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
>
>
> bmmothan at ucalgary.ca wrote:
>> Hello Gromacs users,
>>
>> I am trying to do a free energy calculation, which I have never done
>> before. I have read the manual and the tutorial on the wiki but there
>> is
>> still some issues not clear to me.
>>
>> I am trying to calculate free energy difference of pulling the ligand
>> from
>> a beta-sheet receptor. I understand there is a pull code with different
>> options or it can be done with constraint distances.
>>
>> Please correct me if my procedure is wrong: I want to constraint
>> several
>> distances between the ligand and the receptor and then  increase that
>> distance to one where the ligand and receptor are completely separated.
>> For that, I would have to modify my topology where i define [
>> constraints
>> ] for the distances i want to constrain between the ligand and the
>> receptor and input the bond length for state A(lamda=0) and state B
>> (lamda=1) for each.
>>
>> will the distances defined move the whole ligand away from the
>> receptor?
>> since am only defining several distances between ligand and receptor
>> only.
>>
>> or is it recommended to use the pull code?
>>
>> Any directions is appreciated.
>>
>> Belquis
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>> .
>>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>