[gmx-users] How to apply position restrain on selected atoms in .gro files in Gromacs?
Debashish Banerjee
deb.aerospace at gmail.com
Wed May 6 00:41:12 CEST 2020
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 <jalemkul at 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
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
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--
*Best Regards*
*Debashish Banerjee*
*Ph.D. (Nuclear Materials, Subatech)*
*MS(Sustainable Nuclear Engineering)*
*Advance Nuclear Waste Management*
*Institut Mines-Telecom, **France*
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