[gmx-users] free energy of methan disappearing:tutorial

[mohsen ramezanpour]

Dear Mustard
Thanks very much for your useful notes and your reply
Mohsen

On Tue, Dec 28, 2010 at 7:48 PM, TJ Mustard <mustardt at onid.orst.edu> wrote:

>  Yeah there is so much to do.
>
> 1. Build a methane in a program that allows saving of pdb. Make sure the
> pdb and all the atoms are correctly formated. Or find a methane pdb or gro
> file. I think there is one off of Dr. Mobely's website.
>
>
>
> 2. yes (you don't even need a state_B)
>
>
>
> 3. no (gromacs 4.5.x will take care of it if you setup your mdp file
> correctly)
>
>
>
> 4. All you need to do is read the free energy perturbation section in the
> manual. You will change the settings of your mdp file (under fep) and your
> off. I got some rather nice values.
>
>
>
> I know "read the manual" is the go to phrase here, but it works 95% of the
> time for me.
>
>
>
>
>
> On December 21, 2010 at 2:08 AM mohsen ramezanpour <
> ramezanpour.mohsen at gmail.com> wrote:
>
>  Dear All
>
> I want to calculate protein-drug binding free energy.
> I read Dr.Mobley tutorial(about free energy of  methan dissapearing from
> water).I couldn't understand some of it's parts.
>
> Can I use thisr tutorial in this case(protein-drug)?
>
> Besides, I have a few question about that:
> 1-What do I need to use as my .top & .gro files in my commands?(with
> regarding my problem)docked state or separated state?for example he has used
> methan(separated from water).
> 2-Are these files(.top & .gro) the same for all values of lambda?
> 3-Do these files(.top & .gro)change if you inversed the meaning of lambda=1
> & lambda=0?
> 4-How did he define for (with which parameters) Gromacs  that lambda=1 is
> relating to completely interacting & lambda=0 is relating to methan
> disappearing system?
>
> Please let me know the answer of my questions
> Thank in advance for your reply
> Sincerely yours
> Mohsen
>
>
>
> TJ Mustard
> Email: mustardt at onid.orst.edu
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101228/7bf7fcd8/attachment.html>