Hi Li,

In my opiniun, what you propose is acceptable, but not rigorous, and you will need to prove that there are no unexpected artifacts of changing box size. For example, you should definitely run a couple of your small box systems as larger boxes as well and show that you get the same histograms for the distances between your polyatomic particles.

Justin is correct about the need for a box that is 2x larger than your displacement, and pull_pbcatom is an important option to set as well.

Chris.

Li Jianguo wrote:
Hi
I am trying to calcualte the potential of mean force between two polyatomic particles using umbrella potential and the g_wham command. I need to run multiple windows from close to far inter-particle distance. To save time, I used smaller box sizes for those windows with shorter inter-particle distance, and larger box sizes for those windows with longer inter-particle distance. Then I have multiple pullf files and tpr files with different box sizes. I am wondering if using different simulation systems is acceptable when applying g_wham command for PMF calculation.


I have never heard of such a thing. Is the restraint distance always less than
1/2 the box dimension in the pulling direction?  If not, then this approach
doesn't work.

I have always been under the impression that when running umbrella sampling, you have to actually be doing sampling in different regions of configurational space in the same system, in order to get a continuous energy function and appropriate
sampling.

-Justin


--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to