Dear Gromacs users,
I am trying to set-up my DMPC-TIP3 system for QM/MM studies.
In the attached snapshot, I created the link atom between C-C as shown. Since there are 2 DMPC considered for QM/MM, so I’ll be having two link atoms.
I am using gromacs-2019 patched with DFTB+.
While running grompp, I am getting the following error:
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ERROR: Cannot have constraint (1-2) with virtual site (1)
ERROR: Cannot have constraint (1-6) with virtual site (1)
ERROR: Cannot have constraint (1-10) with virtual site (1)
Program: gmx grompp, version 2022-dev-20201210-8646cc03ad-unknown
Source file: src/gromacs/gmxpreprocess/vsite_parm.cpp (line 975)
Fatal error:
There were 3 virtual sites involved in constraints
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Following is the method which I followed:
1). Inserted two link atoms in the gro file (line number 15107, 15108)
2). Created an itp file for link atom.
3). Created another itp for DMPC (renamed as DMPX) where I did charge redistribution and changed the type of bonded interaction of the selected atoms.
4). Created the dummy section in DMPX (as dummies2).
5). Included “LA” in the atomtypes section of the both “ffnonbonded.itp” and “forcefield.itp”
Here is my topology file section
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#include “toppar/forcefield.itp”
#include “toppar/DMPC.itp”
#include “toppar/DMPC-QM.itp”
#include “toppar/link-atom.itp”
#include “toppar/TIP3.itp”
[ system ]
; Name
Title
[ molecules ]
; Compound #mols
DMPC 126
DMPX 2
LA 2
TIP3 5738
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The LA will be placed between atom C11 (QM) and C12 (MM) of the DMPX.
I am also attaching two more snapshots:
1). Definition of LA in the “atomtypes” section
2). Dummies2 and constraints section defining LA and DMX atoms.
I would greatly appreciate any assistance in this regard.
Thanks in advance.
topol.top (488 Bytes)
nvt.mdp (1.9 KB)