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

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Tue Dec 21 11:08:17 CET 2010


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
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