> Date: Wed, 11 Apr 2012 08:38:05 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] g_wham problem with negative COM differences > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4f857b2d.3050...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Anni Kauko wrote: > > Hi! > > > > I try to perform pmf calculations for case where a peptide shifts > > through the membrane. My COM differences should vary from 2.3 to -2.5. > > > > My problem is that g_wham plots negative COM difference as they would be > > positive. In pullx-files the COM differences are treated correctly > > (look below). My peptide is not symmetric, so profile curves are not > > symmetric, so loosing the sign for COM difference screws my profile > > curve completely. > > > > I did not manage to find any pre-existing answers to this problem from > > internet. > > > > First datalines from pullx files: > > (sorry for strange file names...) > > > > pull_umbr_0.xvg: > > 0.0000 6.26031 2.27369 > > > > pullz_umbr_23.xvg: > > 0.0000 6.09702 0.0233141 > > > > pullz_umbr_50.xvg: > > 0.0000 6.02097 -2.50088 > > > > g_wham command: > > g_wham -b 5000 -it tpr_files.dat -ix pullz_files.dat -o > > profile_test.xvg -hist histo_test.xvg -unit kCal > > > > My pull code: > > > > pull = umbrella > > pull_geometry = distance > > pull_dim = N N Y > > pull_start = yes > > pull_ngroups = 1 > > pull_group0 = POPC_POPS ; reference group is bilayer > > pull_group1 = C-alpha_&_r_92-94 ; group that is actually pulled > > pull_init1 = 0 > > pull_rate1 = 0.0 > > pull_k1 = 1000 ; kJ mol^-1 nm^-2 > > > > Your problem stems from the use of "distance" geometry. This method > assumes the > sign along the reaction coordinate does not change, i.e. always positive or > always negative. If the sign changes, this simple method fails. You > should be > using something like "position" to allow for a vector to be specified. > Perhaps > you can reconstruct the PMF by separately analyzing the positive restraint > distances and negative restraint distances (note here that "distance" > really > refers to a vector quantity, and thus it can have a sign), or otherwise > create > new .tpr files using "position" geometry, though I don't know if g_wham > will > accept them or not. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > Thank's!
I managed to solve my g_wham problem by doing two things: 1. New tpr-files with proper pull code for g_wham. 2. I also needed to modify signs of pullf values: If value for pullx distance was negative, I reversed the sign of corresponding pullf value. I did that by my own script. The new pull code: ; Pull code pull = umbrella pull_geometry = direction pull_vec1 = 0 0 1 pull_start = yes pull_ngroups = 1 pull_group0 = POPC_POPS ; reference group is bilayer pull_group1 = C-alpha_&_r_92-94 ; group that is actually pulled pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 I am little bit confuced, why I needed to tweak signes of pullf values. But like that I got the curve that resembles two half curve made for positive and negative pullx distances separately. That curve also makes sense from biochemical point of view. -Anni PS. Thank's for your excellent tutorials. They have been indispensable help for me to get started with gromacs! -- ************************************************ Anni Kauko, Ph.D. Post Doctoral Researcher Structural Bioinformatics Laboratory Dept. of Biosciences, Biochemistry Åbo Akademi University 20520 Turku, Finland phone: +358 (0)2 215 4006 mobile: +358 (0)50-576 8656 ************************************************
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