On 10/17/19 2:09 PM, Rabeta Yeasmin wrote:
Dear GROMACS users, I am a new user of GROMACS. I am trying to calculate PMF for the translocation process of a protein through lipid bilayer. I have set up total 61 windows above and below the lipid bilayer with a gap of 2A and run umbrella sampling simulation for 100ns, using a force constant of 3 kcal/mol.A2. But after trying to combine results in wahm, I am getting something like this- -5.901639e+01 -nan -5.704918e+01 -nan -5.508197e+01 -nan -5.311475e+01 -nan No PMF value is showing for the windows. I am using the following command to run wham- gmx_mpi wham -it tpr-files.dat -if pullf-files.dat -bins 61 -temp 313.15 -min -60 -max 60 -o -hist -unit kCal Can anyone please help me why I am getting this kind of error?
Usually this means you have no sampling in that region of the reaction coordinate. Check your histograms.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
