Hi, Justin You are right. Finally, I got both of the curves. Happy! Thanks for your guidance.
-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Justin Lemkul Sent: Wednesday, 22 April 2015 10:18 PM To: [email protected] Subject: Re: [gmx-users] g_wham error in umbrella simulation On 4/22/15 4:46 AM, Ming Tang wrote: > Hi, Justin > > Thanks a lot. Dos2unix works. There is even no blank space in every > line. The problem is that I downloaded those .dat files from the > internet, which were created in windows system. But I got another > problem. Following your umbrella sampling tutorial, I got the PMF > curve. The trend of the curve is quite close to that of the curve in > the tutorial. But, the ΔG is -31, 20 more compared to > -50.5 in the tutorial. Besides, I only get one histogram, the data of > the You won't get the value in the tutorial unless you follow the published protocol. The tutorial is an abbreviated version of a more complex protocol involving (1) prior simulation of 100 ns and (2) asymmetrical window distribution. I believe this should be stated already in the tutorial. > rest histograms are zero (one horizontal line). Do you have any > suggestions for me about what's wrong with my simulation? You're probably just not plotting the histogram file right. xmgrace -nxy histo.xvg to show all the histograms. -Justin -- ================================================== 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 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
