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 rest histograms are zero (one horizontal line). Do you have any suggestions for me about what's wrong with my simulation? Thank you.
-----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Monday, 20 April 2015 10:17 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] g_wham error in umbrella simulation On 4/19/15 9:53 PM, Ming Tang wrote: > Dear all, > > I am doing an umbrella simulation, and come across the following error. > > Command line: > g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b > 2000 > > Found 27 tpr and 27 pull force files in tpr-files.dat and > pullf-files.dat, respectively Reading 13 tpr and pullf files Automatic > determination of boundaries... > > ------------------------------------------------------- > Program g_wham, VERSION 5.0.4 > Source code file: > /home/tm/Downloads/gromacs/src/gromacs/gmxana/gmx_wham.cpp, line: 1767 > > Fatal error: > . Should be tpr, xvg, or pdo.0.tpr > Is this a copy/paste problem or is this really what the line said? The error message should be "Unknown file of type (something). Should be tpr, xvg, or pdo." Note the "0.tpr" that is tacked on to the end and the lack of preceding text. Any weird line endings in your tpr-files.dat file? Check and run dos2unix if needed. The presence of "0.tpr" somewhat suggests the very first line is causing a problem, even though it appears gmx wham understands how many files it should find; it just can't determine the right file names/types. -Justin > For more information and tips for troubleshooting, please check the > GROMACS website at http://www.gromacs.org/Documentation/Errors > > tpr-files.dat: > umbrella0.tpr > umbrella137.tpr > umbrella155.tpr > umbrella163.tpr > umbrella169.tpr > umbrella174.tpr > umbrella179.tpr > umbrella185.tpr > umbrella199.tpr > umbrella206.tpr > umbrella223.tpr > umbrella239.tpr > umbrella257.tpr > umbrella275.tpr > umbrella291.tpr > umbrella308.tpr > umbrella324.tpr > umbrella344.tpr > umbrella369.tpr > umbrella383.tpr > umbrella392.tpr > umbrella422.tpr > umbrella450.tpr > umbrella463.tpr > umbrella479.tpr > umbrella497.tpr > umbrella499.tpr > > pullf-files.dat > pullf0.xvg > pullf137.xvg > pullf155.xvg > pullf163.xvg > pullf169.xvg > pullf174.xvg > pullf179.xvg > pullf185.xvg > pullf199.xvg > pullf206.xvg > pullf223.xvg > pullf239.xvg > pullf257.xvg > pullf275.xvg > pullf291.xvg > pullf308.xvg > pullf324.xvg > pullf344.xvg > pullf369.xvg > pullf383.xvg > pullf392.xvg > pullf422.xvg > pullf450.xvg > pullf463.xvg > pullf479.xvg > pullf497.xvg > pullf499.xvg > > I used this method several times before, and did not come across this > problem. could anybody tell me where is the problem? > Thanks > -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org. -- 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 gmx-users-requ...@gromacs.org.