[gmx-users] Umbrella sampling windows

Laura Kingsley lkingsle at purdue.edu
Tue Feb 15 16:06:16 CET 2011

Hello Susana,

I agree with Justin, 3000 kj/molnm2 seems pretty high. I've been using 
about a 1000kj/molnm2 force constant with window separation of about 
0.8, that seems to work well for my system.


On 02/15/2011 09:51 AM, Susana Tomasio wrote:
> Hi all,
> I'm running umbrella sampling of an ion through a lipid bilayer with 
> gromacs 4.5.1.
> I used g_wham to create the histograms of the configurations within 
> the umbrella sampling windows (1 Angstrom interval).
> I did not get a sufficient overlap between the windows, so I was 
> wodering which is the better way of increasing the sampling:  to
>  include additional windows in the regions where there is no overlap 
> or to increase the force constant ?
> If I increase the force constant can I continue the simulation with 
> the new constant or do I have to start again?
> I used a force contant of 3000 kJ mol^-1 nm^-2.
> Thank you in advance,
> Susana

Laura Kingsley

Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University
Office: RHPH 504A
575 Stadium Mall Dr.
West Lafayette, IN 47907
Office Phone: (765) 496-6643

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110215/adb2fb03/attachment.html>

More information about the gromacs.org_gmx-users mailing list