[gmx-users] Strange dV/dl profile in free energy calculation

Maik Goette mgoette at mpi-bpc.mpg.de
Wed Jul 9 10:10:44 CEST 2008


Always hard to tell, cause one doesn't know, if your parameters are 
correct ;)

Anyway, the LJ-part always looks a bit unintuitive, probably due to 
softcore. I saw similar curves in my base-deletions. I think, you can 
trust the curve.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2305
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Robert Johnson wrote:
> Hello everyone,
> Sorry if you get this twice. It seems to me that the previous message
> didn't go through.
> I'm computing the binding free energy of DNA bases (just the base, no
> sugar, no phosphate) on a carbon
> nanotube following the prescirption of the Dill group Wiki
> (http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial)
> and the Boresch paper (J. Phys. Chem. B., 107, 9535, 2003). I split my
> calculation up into two parts. In the first part, I turn off all the
> charges in my DNA base (guanine in this case). In the second part, I
> turn off all the LJ parameters. I run MD at each lambda value for 15
> ns. An image of the dV/dl plot obtained from the previous
> simulations is located here:
> http://dept.physics.upenn.edu/~robertjo/public_files/gmx/dvdl.jpg The
> error bars are included in the graph (they are very
> small...less than 1 kJ/mol in all cases).
> My concern is the dV/dl curve for turning off the LJ parameters (i.e.
> making the base "disappear") looks fairly strange. First it increases
> and then decreases to a minimum value at lambda=0.8, and then
> increases again. This looks significantly different than the identical
> curve for disappearing a methane molecule in water:
> http://dept.physics.upenn.edu/~robertjo/public_files/gmx/dgdl_methane.jpg
> The methane calculation followed the steps discussed in the Dill group
> Wiki and agrees with the result reported there. Is there anyone who
> has some experience performing these calculations that can comment on
> my curve for the DNA base? Does my curve look reasonable?
> Thanks,
> Bob Johnson
> _______________________________________________
> 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
> .

More information about the gromacs.org_gmx-users mailing list