Just a small rectification: *posres_Cs.itp* were created and used every time. I mistakenly wrote posre_Cs.itp while typing it here, my bad.
Thanks, Debashish On Tue, May 5, 2020 at 11:54 PM Debashish Banerjee <deb.aerosp...@gmail.com> 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. > > There were 2 notes > ------------------------------------------------------- > Program: gmx grompp, version 2016.4 > Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1880) > > Fatal error: > There was 1 error in input file(s) > > > Kindly help me fix it please. > > With lots of hope of finding an answer.... > -- > *Best Regards* > > *Debashish Banerjee* > > *Ph.D. 3rd year (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? 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