[gmx-users] force constants for umbrellla histograms
x.periole at rug.nl
Fri Aug 20 21:55:40 CEST 2010
The most important is that you have to put in trajectories that
are equilibrated! You can mix as much force constant values
you like but always equilibrated ...
Then the lower the force constant the longer the simulation needs
to be to reach equilibrium: larger conformational space accessible.
I can also imagine that a too strong force constant might deform
your molecules in a manner you should not.
> Then does it matter how many times you vary it, and how large ?
> In my
> sampling I have very good histograms up to 2 nm (force constant = 1000
> kj/mol), above 2nm they are not. I feel I may have to use a force
> constant of 500 for the next 3 or 4 windows, and even less again
> (ca~ 50
> kj/mol) beyond that.
> XAvier Periole wrote:
>> On Aug 20, 2010, at 5:12 PM, Gavin Melaugh wrote:
>>> Hi all
>>> Is is O.K to use different force constants for different sampling
>>> windows for the generation of the potential of mean force curves?
>>> Many Thanks
>>> -- gmx-users mailing list gmx-users at gromacs.org
>>> Please search the archive at http://www.gromacs.org/search before
>>> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before
> 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