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. Regards, Debashish On Wed, May 6, 2020 at 12:40 AM Debashish Banerjee <deb.aerosp...@gmail.com> wrote: > Thank you Justin, you are a life saver..!!!!! > It's working now. You have correctly pointed out the issue. > Thank you so much...... :) > > Regards, > Debashish > > On Wed, May 6, 2020 at 12:11 AM Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 5/5/20 5:54 PM, Debashish Banerjee wrote: >> > Dear gmx users, >> > >> > I have been stuck in a problem for a month now and have scrutinized all >> the >> > past discussions and forms related to it dating as back as 9 years. Now >> I >> > really need your help. >> > >> > My system has Clays (layered philosillacates), Cesium ions (Cs), acetate >> > molecules as well as water. In total 24241 atoms in the whole system. I >> > want to perform free energy calculations *(PMF)* via *umbrella >> sampling*. >> > >> > The whole idea is that I want to fix one Cs atom (atom number/index >> number~ >> > 5790) near to the basal surface (top layer) of clay and put in use of >> the* >> > pull* code as described in umbrella sampling and thereafter perform >> *WHAM* >> > calculations to see the progression of COM distance between (Cs) and >> the >> > surface oxygen's present on the top layer of clay sheet over time. >> > >> > When, I see it in my .gro files, I can find all 16 Cs atoms ranging from >> > index number (5785-5780). I just want to fix a particular single Cs atom >> > (index number 5790) as mentioned above. For this I create a special >> index >> > file which now has an extra group containing just 1 Cs atom. After >> this, I >> > take in the use of gmx genrestr command : >> > *gmx genrestr -f npt.gro -n index.ndx -o posre_Cs.itp -fc 0 0 1000* >> > This commands redirects to the newly created group from the index file >> > which I created above and put constraints in it. >> > >> > *Step 1 * >> > The *posre_Cs.itp* file looks like this: >> > [ position_restraints ] >> > ; i funct fcx fcy fcz >> > 5790 1 0 0 1000 >> > >> > * Step 2 * >> > *My topology should include an if statement, so I also define it like >> this:* >> > >> > #include "../charmm36.ff/forcefield.itp" >> > >> > ; include params for ClayFF >> > #include "../ClayFF.ff/ffnonbonded.itp" >> > >> > ; Include topology for Clay Montmorillonite (MMT) >> > #include "../ClayFF.ff/MMT_UC/UC2.itp" >> > #include "../ClayFF.ff/MMT_UC/UC1.itp" >> > #include "../ClayFF.ff/MMT_UC/UC3B.itp" >> > #include "../ClayFF.ff/MMT_UC/UC3T.itp" >> > >> > ; Added the part of defining ions.itp which contains Cs atom and defined >> > position restrain parameters >> > >> > >> > >> > >> > *#include "../ClayFF.ff/ions.itp"#ifdef POSRES_Cs#include >> > "posres_Cs.itp"#endif* >> > #include "../charmm36.ff/spc.itp" >> > >> > #include "../charmm36.ff/organics/act.itp" >> > >> > [ system ] >> > ; Name >> > clay + Cs + acetate + water >> > >> > [ molecules ] >> > ; Compound #mols >> > UC2 1 >> > UC1 1 >> > UC3B 1 >> > UC2 1 >> > UC2 1 >> > UC1 1 >> > UC1 1 >> > UC2 1 >> > UC2 1 >> > UC3T 1 >> > UC1 1 >> > UC2 1 >> > UC2 1 >> > UC3B 1 >> > UC3T 1 >> > UC2 1 >> > UC2 1 >> > UC1 1 >> > UC3B 1 >> > UC2 1 >> > UC2 1 >> > UC1 1 >> > UC1 1 >> > UC2 1 >> > UC2 1 >> > UC3T 1 >> > UC1 1 >> > UC2 1 >> > UC2 1 >> > UC3B 1 >> > UC3T 1 >> > UC2 1 >> > Na 24 >> > SOL 312 >> > UC2 1 >> > UC1 1 >> > UC3B 1 >> > UC2 1 >> > UC2 1 >> > UC1 1 >> > UC1 1 >> > UC2 1 >> > UC2 1 >> > UC3T 1 >> > UC1 1 >> > UC2 1 >> > UC2 1 >> > UC3B 1 >> > UC3T 1 >> > UC2 1 >> > UC2 1 >> > UC1 1 >> > UC3B 1 >> > UC2 1 >> > UC2 1 >> > UC1 1 >> > UC1 1 >> > UC2 1 >> > UC2 1 >> > UC3T 1 >> > UC1 1 >> > UC2 1 >> > UC2 1 >> > UC3B 1 >> > UC3T 1 >> > UC2 1 >> > Na 24 >> > SOL 312 >> > UC2 1 >> > UC1 1 >> > UC3B 1 >> > UC2 1 >> > UC2 1 >> > UC1 1 >> > UC1 1 >> > UC2 1 >> > UC2 1 >> > UC3T 1 >> > UC1 1 >> > UC2 1 >> > UC2 1 >> > UC3B 1 >> > UC3T 1 >> > UC2 1 >> > UC2 1 >> > UC1 1 >> > UC3B 1 >> > UC2 1 >> > UC2 1 >> > UC1 1 >> > UC1 1 >> > UC2 1 >> > UC2 1 >> > UC3T 1 >> > UC1 1 >> > UC2 1 >> > UC2 1 >> > UC3B 1 >> > UC3T 1 >> > UC2 1 >> > Na 24 >> > Cs 16 >> > act 16 >> > SOL 6103 >> > >> > *Step 3* >> > In my mdp file, I defined it as follows: >> > *define = -DPOSRES_Cs* >> > >> > >> > *The problem : * >> > gmx_mpi grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr >> > >> > Setting the LD random seed to 1967282441 >> > Generated 83825 of the 83845 non-bonded parameter combinations >> > Generating 1-4 interactions: fudge = 1 >> > Generated 57459 of the 83845 1-4 parameter combinations >> > >> > ERROR 1 [file posres_Cs.itp, line 5]: >> > Atom index (5790) in position_restraints out of bounds (1-1). >> > This probably means that you have inserted topology section >> > "position_restraints" in a part belonging to a different molecule >> than >> > you intended to. >> > In that case move the "position_restraints" section to the right >> molecule. >> >> >> http://manual.gromacs.org/current/user-guide/run-time-errors.html#atom-index-n-in-position-restraints-out-of-bounds >> >> Presumably your Cs+ topology defines the [moleculetype] as having one >> ion in it. Therefore, the only valid atom number in >> [position_restraints] is 1. The global atom numbering is meaningless in >> the context of position restraints (which are assigned at the topology >> level) as genrestr warns you (see the help description; if you're trying >> to restrain anything that isn't the first molecule, you can't use it). >> >> The solution is to define a new [moleculetype] for the Cs+ ion you want >> to restrain, and use >> >> [position_restraints] >> 1 1 0 0 1000 >> >> in its topology. >> >> -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. > > > > -- > *Best Regards* > > *Debashish Banerjee* > > *Ph.D. (Nuclear Materials, Subatech)* > *MS(Sustainable Nuclear Engineering)* > *Advance Nuclear Waste Management* > *Institut Mines-Telecom, **France* > -- *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.
