On Jun 1, 2010, at 9:13 PM, Ozge Engin wrote:
Hi all,
I am trying to calculate the potential of mean force between the two
hydrophobic dipeptides (phenylalanine) in bulk water via constraint
pulling simulations. First, I calculated the mean force at each of
the constraint points, and then I integrated the mean force curve to
get the PMF.
In order to test how big the effect of the number of water molecules
on the calculated PMF I performed two sets of simulations which
differed from each other in terms of only the number of water
molecules. I used 9000 water molecules in one set, and 7000 in the
other. The overall PMF for the latter was steeper than the former,
as I expected before. However, the minimum point for the former was
around 2.79 kJ/mol, and for the latter 5.30 kJ/mol. I did not think
that the difference should not be that much since there is not a big
difference between the number of water molecules between the two sets.
Could it be that the difference is within the error ? What happens if
you
cut your data of each simulation in two pieces? In other words are you
converged?
I searched the internet to find a study regarding the concentration
dependency of the PMF.
Is this reasonable? Any suggestions?
Regards
Ozge Engin
--
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
--
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
