GROMACS version: 2020.1
GROMACS modification: No
Hi all,
I am working with a water system, where some waters around the system’s COM will be flat-bottom restrained, while the rest will be unrestrained. I used CHARMM-GUI to create a water box, which was equilibrated during 1 ns. Then, following a previous suggestion (Setting spherical restraints), I modified the topology of the system to create two topologies for the restrained (TIP3) and unrestrained (TP3R, the name is also changed in the input .gro file) solvents, grouped in an index file.
When I run mdrun, get this error:
Fatal error:
The [molecules] section of your topology specifies more than one block of
a [moleculetype] with a [settles] block. Only one such is allowed.
If you are trying to partition your solvent into different *groups*
(e.g. for freezing, T-coupling, etc.), you are using the wrong approach. Index
files specify groups. Otherwise, you may wish to change the least-used
block of molecules with SETTLE constraints into 3 normal constraints.
If I comment the [ settles ] and [ exclusions ] directives in either molecule, then:
starting mdrun '10A spherical restrained water in a box'
1000000 steps, 1000.0 ps.
step 0
step 1: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
Bellow are the .itp files and the topology.
Unrestrained solvent:
[ moleculetype ]
; name nrexcl
TIP3 2
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 OT 1 TIP3 OH2 1 -0.834000 15.9994 ; qtot -0.834
2 HT 1 TIP3 H1 2 0.417000 1.0080 ; qtot -0.417
3 HT 1 TIP3 H2 3 0.417000 1.0080 ; qtot 0.000
[ settles ]
OW funct doh dhh
1 1 9.572000e-02 1.513900e-01
[ exclusions ]
1 2 3
2 1 3
3 1 2
Restrained solvent:
[ moleculetype ]
; name nrexcl
TP3R 2
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 OT 1 TIP3 OH2 1 -0.834000 15.9994 ; qtot -0.834
2 HT 1 TIP3 H1 2 0.417000 1.0080 ; qtot -0.417
3 HT 1 TIP3 H2 3 0.417000 1.0080 ; qtot 0.000
[ settles ]
OW funct doh dhh
1 1 9.572000e-02 1.513900e-01
[ exclusions ]
1 2 3
2 1 3
3 1 2
#ifdef POSRES_WATER_SPH
[ position_restraints ]
; atom type g r k
1 2 1 1 10000
#endif
“Mini” force field:
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 1.0 1.0
[ atomtypes ]
; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14
HT 1 1.0080 0.417 A 4.00013524445e-02 1.924640e-01
OT 8 15.9994 -0.834 A 3.15057422683e-01 6.363864e-01
[ bondtypes ]
; i j func b0 Kb
HT HT 1 1.513900e-01 0.000000e+00
HT OT 1 9.572000e-02 3.765600e+05
[ pairtypes ]
; i j func sigma1-4 epsilon1-4
HT HT 1 4.00013524445e-02 1.92464000000e-01
HT OT 1 1.77529387564e-01 3.49973530556e-01
OT OT 1 3.15057422683e-01 6.36386400000e-01
[ angletypes ]
; i j k func th0 Kth s0 Kub
HT OT HT 5 1.0452000e+02 4.6024000e+02 0.0000000e+00 0.0000000e+00
Topology:
; Include forcefield parameters
#include "charmm36-jul2020.ff/forcefield.itp"
; Include forcefield parameters for TIP3 water
#include "charmm36-jul2020.ff/TIP3.itp"
; Include forcefield parameters for TIP3 water restrained
#include "charmm36-jul2020.ff/TIP3_restrained.itp"
[ system ]
; Name
10A spherical restrained (10000 kJ-mol_nm2) water in a box
[ molecules ]
; Compound #mols
TIP3 6704
TP3R 137
Attached is the .mdp file:
md_sphere_restrained.mdp (1.2 KB)
Am I missing something? Any help will be appreciated.
Best