GROMACS version:2023
GROMACS modification: No
Understanding that gromacs is not particularly fond of inorganics, I’ve download MgO2 from CHarmm gui, and other than file name changes have run mininmization and equilibration ( nvt ). The runs proceed without error and the output gro files can be loaded visualized in VMD and Samson. However the trajectories do not play in either program. Errors stating that the gro file names and itp file names do not match. A first warning is that I’m using an incorrect top file. The second is that e.g top file MGO001 1 does not match MGO00 1 ( note the end spaces). I do not understand how the simulation could run at all with an incorrect top file
run commands
gmx grompp -f nvt.mdp -c MgO.em -p topol.top -o MgO.nvt
gmx mdrun -deffnm MgO.nvt -nb gpu -pme gpu -ntomp 4 -ntmpi 16 -npme 1 -nsteps 100000
files:
topol.top
;;
;; Generated by CHARMM-GUI FF-Converter
;;
;; Correspondance:
;; jul316@lehigh.edu or wonpil@lehigh.edu
;;
;; The main GROMACS topology file
;;
; Include forcefield parameters
#include “toppar/forcefield.itp”
#include “toppar/NMA.itp”
[ system ]
; Name
Title
[ molecules ]
; Compound #mols
NMA 588
mdp
integrator = sd
dt = 0.001
nsteps = 125000
nstxtcout = 5000
nstvout = 5000
nstfout = 5000
nstcalcenergy = 100
nstenergy = 1000
nstlog = 1000
;
cutoff-scheme = Verlet
nstlist = 20
rlist = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
coulombtype = pme
rcoulomb = 1.2
;
tcoupl = Nose-Hoover ;;;V-rescale
tc_grps = SYSTEM
tau_t = 1.0
ref_t = 298.15
;
constraints = h-bonds
constraint_algorithm = LINCS
;
nstcomm = 100
comm_mode = linear
comm_grps = SYSTEM
;
gen-vel = yes
gen-temp = 298.15
gen-seed = -1
;
refcoord_scaling = com
----------------------- first few lines of MgO.em input and MgO ouput to the mdp:
Generated by CHARMM-GUI FF-Converter
4704
1MGO00 MG1 1 1.502 1.502 1.518
1MGO00 O1 2 1.713 1.713 1.729
1MGO00 O2 3 1.502 1.502 1.729
1MGO00 O3 4 1.502 1.713 1.518
1MGO00 O4 5 1.713 1.502 1.518
1MGO00 MG2 6 1.713 1.713 1.518
1MGO00 MG3 7 1.713 1.502 1.729
1MGO00 MG4 8 1.502 1.713 1.729
2MGO00 MG1 9 1.502 1.923 1.518
2MGO00 O1 10 1.713 2.134 1.729
2MGO00 O2 11 1.502 1.923 1.729
2MGO00 O3 12 1.502 2.134 1.518
2MGO00 O4 13 1.713 1.923 1.518
–from the nvt run
Title
4704
1MGO00 MG1 1 1.593 1.450 2.103 -0.1622 0.0359 -0.1649
1MGO00 O1 2 1.819 1.656 2.262 0.5920 -0.3201 0.5994
1MGO00 O2 3 1.630 1.428 2.304 -0.3142 0.0536 -0.0286
1MGO00 O3 4 1.569 1.649 2.096 -0.0515 -0.0965 0.3830
1MGO00 O4 5 1.793 1.443 2.067 -0.4001 -0.4511 -0.3286
1MGO00 MG2 6 1.782 1.647 2.062 0.2470 0.2323 -0.7284
1MGO00 MG3 7 1.835 1.432 2.267 -0.5341 -0.2154 0.3629
1MGO00 MG4 8 1.616 1.643 2.300 0.4648 -0.0575 -0.1238
2MGO00 MG1 9 1.590 1.847 2.091 0.4216 -0.2477 -0.0898
2MGO00 O1 10 1.788 2.072 2.256 0.4411 -0.2090 0.2790
At what is such a modification of the atom names made ?