Hello gmx users, I am stuck at a very basic command line and need your expertise in dealing through it.
Basically, I have a clay sheet containing 192 surface oxygen. Since I am doing umbrella sampling for PMF calculations, I want to get the progression of COM distances of my fixed Cs atom from the center of mass of the clay sheet (basically these 192 surface oxygen) over time. I have already created special index file which has relevant groups such as ; group 18 --> *referenceSurface* ~containing 192 surface oxygen group 19 --> *restrainedCs* ~containing 1 Cs atom (basically the one that I have fixed) group 20 --> another Cs atom (this one is not fixed and can move freely in all sample space during the entire course of simulation) Command line: *Case 1* *gmx_mpi distance -n index.ndx -f conf0.gro -s pull.tpr -select 'com of group 19 plus com of group 18' -oxyz dist00.xvg* Inconsistency in user input: Invalid index group reference(s) Group 'referenceSurface' cannot be used in selections except as a full value of the selection, because atom indices in it are not sorted and/or it contains duplicate atoms. *Case 2* *gmx_mpi distance -n index.ndx -f conf0.gro -s pull.tpr -select 'com of group 19 plus com of group 20' -oxyz dist2.xvg* Reading file npt.tpr, VERSION 2016.4 (single precision) Reading frames from gro file 'Generated by trjconv : clay + Cs + acetate + water t= 2.00000', 24221 atoms. Last frame 0 time 2.000 Analyzed 1 frames, last time 2.000 com of group 19 plus com of group 20: Number of samples: 1 Average distance: 0.52370 nm Standard deviation: 0.00000 nm My understanding is that if I compare the above 2 cases, I would say that for *case 2*, Cs is measuring it's distance from the only other Cs atom. No problem here, whereas for *case 1*, Cs atom is measuring it's distance from all 192 oxygen atoms, somehow not understanding how to take the center of mass of the whole sheet containing 192 atoms. Approach taken: 1. Modified my command line from this: gmx_mpi distance -s pull.tpr -f conf0.gro -n index.ndx -select 'com of group "restrainedCs" plus com of group "referenceSurface"' -oall dist0.xvg 2. Used all output options like -oav / -oxyz I have followed the following threads, but still couldn't manage to rectify this error https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg16576.html https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg30552.html Please help. I am pretty much sure that I am overseeing a very basic step. -- *Best Regards* *Debashish Banerjee* *Ph.D. (Nuclear Materials, Subatech)* *MS(Sustainable Nuclear Engineering)* *Advance Nuclear Waste Management* *Institut Mines-Telecom, **France* -- 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.
