[gmx-users] Strange in PMF calculation (Shi Li)

Justin Lemkul jalemkul at vt.edu
Thu Nov 24 00:00:06 CET 2016

Please don't reply to the entire digest.

On 11/22/16 7:29 PM, Shi Li wrote:

>> On 11/22/16 3:14 PM, Li, Shi wrote:
>>> Dear Gromacs users,
>>> I am doing some PMF simulations of 2 molecules in vacuum and my resulting
>>> profile has a strange look. I attached an eps files here, anyone can give
>>> me some suggestion on why there is fluctuation at longer distance?
>> The mailing list does not accept attachments.  Upload an image to a file-sharing
>> service and provide the URL.
>> -Justin
> Thank you Justin,
> Here is the link to my eps file.
> https://www.dropbox.com/s/bc2ch1nujm0f825/syn.eps?dl=0 <https://www.dropbox.com/s/bc2ch1nujm0f825/syn.eps?dl=0>

Do you have sufficient sampling?  How is the overlap between the histograms? 
This could just be a small sampling defect.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list