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* -- 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.
