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* -- 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 [email protected].
