Hi all I have a question on dealing with two reaction coordinates by gmx_wham. I did umbrella sampling on glucose 6-phosphate molecule on a poly-Lys peptide surface. Because the peptide is neither cylindrical nor spherical symmetric, I have to restraint each window around a specific point, using two reaction coordinates (distance and direction). As results, the ligand's trajectory looks pretty well. It was restraint around a specific points, instead of going around a sphere surface when I used 'distance' alone.
However, I got some issue using WHAM for analysis. That is, GROMACS seems not to allow me to use WHAM with two pull geometry (distance and direction). So I have to pick only one reaction coordinate to do the analysis. When I run regular wham, I got this issue: Fatal error: umbrella0.tpr: Your pull coordinates have different pull geometry (coordinate 1: distance, coordinate 2: direction) If you want to use only some pull coordinates in WHAM, please select them with option gmx wham -is I refer this link to pick one of the two reaction coordiantes to work on WHAM. https://urldefense.proofpoint.com/v2/url?u=http-3A__manual.gromacs.org_documentation_2016_onlinehelp_gmx-2Dwham.html&d=DwIFaQ&c=nE__W8dFE-shTxStwXtp0A&r=gCy395jfSTIKIGBjdJ8SwSg8yN7wywRqF0ilx8ZoefpMNPZKIUY0jXzHKcFUwcQV&m=ylMBZcLbqfFPYBVa5g85k4Po5Oxm2FUPBpXKM3fIYYY&s=UAqEj3Fxkq5Wq5wgDTU6IGriSSwUWc8o1emqkL1sQ-s&e= See all the figures in this link: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.evernote.com_l_AAMsNYa6HXZFeqNDTbsiV4HO0ta2KY-2Dnz7s_&d=DwIFaQ&c=nE__W8dFE-shTxStwXtp0A&r=gCy395jfSTIKIGBjdJ8SwSg8yN7wywRqF0ilx8ZoefpMNPZKIUY0jXzHKcFUwcQV&m=ylMBZcLbqfFPYBVa5g85k4Po5Oxm2FUPBpXKM3fIYYY&s=kcFXCPX23_hqHOKeQ3iV61pQ_i0PFkuIsB5K1jKT-Co&e= When I only selected 'distance' for WHAM, the histogram and PMF looks like this (Figure 1). I can somewhat understand the insufficient overlap at 0.5-0.75 nm could result in some abnormal segment in PMF, but what really confused me is the global decreasing on PMF. Then histogram looks just right. Here is the result when only selecting 'direction' as the reaction coordinate for wham (Figure 2). Gromacs's WHAM still output the distance as x-axis, and the histogram is different form the above one. Then I just simply add these two PMFs together and got following plots. (Figure 3) The summation looks like what I expected. I can not understand this. Because the restraints by 'distance' and 'direction' are perpendicular to each other, the coordinate-1's WHAM result should be something like what I got from single reaction coordinate. I expected the coordinate-1's WHAM result should look like the summation result. I do not have experience on dealing with two reaction coordinates. So, I will appreciate it if anybody has suggestions on how to figure this out. Here is the pulling parameter for my umbrella sampling: Pull code pull = yes pull_ngroups = 2 ; there are two pulling groups pull_ncoords = 2 ; two reaction coordiante to restraint the molecule around its initial position pull_group1_name = Other ; ligand pull_group2_name = ref_group . reference group, it is a part of my peptide ; first reaction coordinate pull_coord1_type = umbrella ; harmonic biasing force pull_coord1_geometry = distance ; simple distance increase pull_coord1_groups = 1 2 ; two groups the pulling will be applied pull_coord1_dim = Y Y Y pull_coord1_rate = 0.0 ; 0.01 nm per ps = 10 nm per ns pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 ; second reaction coordinate pull_coord2_type = umbrella ; harmonic biasing force pull_coord2_geometry = direction ; simple distance increase pull_coord2_vec = 11.018 -20.969 13.824 pull_coord2_groups = 1 2 pull_coord2_dim = Y Y Y pull_coord2_rate = 0.0 ; 0.01 nm per ps = 10 nm per ns pull_coord2_k = 1000 ; kJ mol^-1 nm^-2 pull_coord2_start = yes ; define initial COM distance > 0 Best Yuanchao Liu (εε θΆ ) Ph.D. Candidate Department of Chemical Engineering and Materials Science 428 South Shaw Lane, Room 3263 Michigan State University East Lansing, Michigan 48824-4437 Email: ycliu1...@gmail.com; liuyu...@msu.edu; liuyu...@egr.msu.edu Cell:+1 (517)-763-1806 -- 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.