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.
