Dear Justin, Thanks for your reply. I checked the content in pullx.xvg file as follows: -------------------------------------------------------- # GRowing Old MAkes el Chrono Sweat # @ title "Pull COM" @ xaxis label "Time (ps)" @ yaxis label "Position (nm)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "0 Z" @ s1 legend "1 dZ" 0.0000 6.50285 -0.206062 10.0000 7.66133 -2.6497 20.0000 7.65877 -2.65375 30.0000 7.65128 -2.6575 40.0000 7.64102 -2.66939 --------------------------------------------------------------
The numbers in 1st column is time. What is the meaning of the numbers in the 2nd and 3rd columns? Many thanks. Mingjun ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul [jalem...@vt.edu] Sent: Thursday, September 12, 2013 10:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] umbrella sampling using pull codes On 9/12/13 9:55 AM, mjyang wrote: > Dear GMX users, > > I'd like to perform the umbrella sampling using the pull codes in > gromacs. The reaction coordinate is defined as the distance between the > center of mass (DCOM) of two domains in a protein. The following script is > used: > ------------------- only for pull section > ; Pull code > pull = umbrella > pull_geometry = distance > pull_dim = N N Y > pull_start = no > pull_ngroups = 1 > pull_group0 = NN1 ; contained in index file > pull_group1 = NN2 ; contained in index file > pull_init1 = 2.5 > pull_rate1 = 0.0 > pull_k1 = 20000 ; kJ mol^-1 nm^-2 > pull_nstxout = 5000 ; every 2 ps > pull_nstfout = 5000 ; every 2 ps > ----------------- > > I have two questions about the output of gromacs: > 1. How is the energy term "COM Pull En." in *.log file calculated? Is it > computed as 1/2*kf*(DCOM_t - pull_init1)^2 at time t? Sounds right. It's something that's very easy to calculate yourself from a given trajectory frame to confirm. > 2. Where is the output information for the evolution of DCOM? Is it in the > file pullx.xvg? > Yes. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
