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
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