How do I combine two topology files of a nano-pore and a water model

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GROMACS version: 2020
GROMACS modification: Yes/No
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Hi I have creates two systems- of an equilibrated water model (TIP4P/2005), and another system of an energy minimsed nanopore. For doing the equilibration of water and energy minimisation of the pore, I have run simulations using their individual topology (.top) files. Now, I have created a system by combining the two (after deleting the overlapping water molecules), to study the dynamics of water inside the confinement.
But, I have been reading the Gromacs manual (chapter 5) for some time, yet was not able to combine the two topology files, into that of the combined system. I tried attaching my individual topology files, but apparently, the system does not allow for new users to attach files.

I would really appreciate if someone can suggest how to do this, and/or point to a discussion if this has already been addressed in the forum!

Thanks in advance :)

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The topoloy file for pore looks like this:

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.833333

[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
SI 14 28.08600 0.000000 A 0.2500 0.0004184
OM 8 15.99940 0.000000 A 0.2700 1.9120880
OA 8 15.99940 0.000000 A 0.3070 0.7112800
HG 1 2.01600 0.000000 A 0.1295 0.0015301

#include “grid.itp”

[ system ]
Pore-System Generated by the PoreMS Package

[ molecules ]
OM 40984
SI 20494
SLX 125
SL 78
SLG 4

The topology file for water looks like this:
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 no 1.0 1.0

[atomtypes]
;name mass charge ptype sigma epsilon
IW 0 0.000 D 0.0 0.0
OWT4 15.9994 0.000 A 0.31589 0.77490
HW 1.0079 0.000 A 0.00000E+00 0.00000E+00

[moleculetype]
; name nrexcl
water 1

[atoms]
; nr type resnr residu atom cgnr charge
1 OWT4 1 water OW1 1 0 15.9994
2 HW 1 water HW2 1 0.5564 1.0079
3 HW 1 water HW3 1 0.5564 1.0079
4 IW 1 water MW4 1 -1.1128 0.0

[constraints]
;i j funct doh dhh
1 2 1 0.09572
1 3 1 0.09572
2 3 1 0.15139

[exclusions]
1 2 3 4
2 1 3 4
3 1 2 4
4 1 2 3

; The position of the dummy is computed as follows:
;
; O
;
; D
;
; H H
;
; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]
; 0.01546 nm / [ cos (52.26 deg) * 0.09572 nm ]

; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)

[dummies3]
; Dummy from funct a b
4 1 2 3 1 0.13193828 0.13193828

[system]
water tip4p/2005

[molecules]
water 360

3

Hello Avimu
I’ve tried to run silica MD pore simulation by POREMS with hexane as a solvent. But I got problem because i can’t get ITP file from silica pore, how to get topology from pore that has been produced by POREMS.

Thanks,Kindly help me!