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

==================================================

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