My structure does not contain any ions. Here are the commands that I used:
gmx_d pdb2gmx -f nm_*.pdb -o pdb2gmx.pdb -p topol.top -ff amber99sb -water
tip3p -ignh
gmx_d editconf -f pdb2gmx.pdb -o editconf.pdb -bt dodecahedron -d 2.5
gmx_d grompp -f cg.mdp -c editconf.pdb -p topol.top -o cg.tpr
gmx_d mdrun -deffnm cg -v
gmx_d grompp -f bfgs.mdp -t cg.trr -c cg.tpr -p topol.top -o bfgs.tpr -maxwarn
1
gmx_d mdrun -deffnm bfgs -v
gmx_d grompp -f nm.mdp -t bfgs.trr -c bfgs.tpr -p topol.top -o nm.tpr
The used mdp files:
cg.mdp :
; Parameters describing what to do, when to stop and what to save
integrator = cg; Algorithm (cg= Conjugate Gradient
minimization)
emtol= 0; Stop minimization when the maximum force <
10.0 kJ/mol/nm
emstep = 0.1 ; Energy step size
nsteps = 50; Maximum number of
(minimization) steps to perform
nstcgsteep = 1000
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
cutoff-scheme = verlet
nstlist= 1 ; Frequency to update the
neighbor list and long range forces
ns_type = grid ; Method to determine
neighbor list (simple, grid)
rlist= 1.4 ; Cut-off for making neighbor
list (short range forces)
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 1.0 ; Treatment of long range
electrostatic interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
vdwtype = cutoff
vdw-modifier= force-switch
rvdw-switch = 1.0
rvdw = 1.2; Short-range Van der Waals cut-off
fourierspacing = 0.12
pme_order = 4
ewald_rtol =1e-09
epsilon_surface = 0
pbc = xyz ; Periodic Boundary Conditions
(yes/no)
bfgs.mdp:
;mdp for l-bfgs energy minimization
define = -DFLEXIBLE
constraints = none
integrator = l-bfgs
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
cutoff-scheme = verlet
nstlist= 10 ; Frequency to update the
neighbor list and long range forces
ns_type = grid ; Method to determine
neighbor list (simple, grid)
rlist= 1.4 ; Cut-off for making neighbor
list (short range forces)
coulombtype = Reaction-Field
coulomb-modifier = potential-shift ; Treatment of long range
electrostatic interactions
rcoulomb-switch = 1.0
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
fourierspacing = 0.12
pme_order = 4
epsilon_surface = 0
ewald_rtol = 1e-9
pbc = xyz ; Periodic Boundary Conditions
(yes/no)
;
; Energy minimizing stuff
;
emtol= 0.0
emstep = 0.0001
nstcgsteep= 1000
nbfgscorr = 10
nsteps = 50
nm.mdp:
;Parameters describing what to do, when to stop and what to save
define = -DFLEXIBLE
integrator =nm ;Algorithm(normal mode)
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
cutoff-scheme = verlet
nstlist= 10 ; Frequency to update the
neighbor list and long range forces
ns_type = grid ; Method to determine
neighbor list (simple, grid)
rlist= 1.4 ; Cut-off for making neighbor
list (short range forces)
coulombtype = Reaction-Field ; Treatment of long
range electrostatic interactions
coulomb-modifier = potential-shift
rcoulomb-switch = 1.0
rcoulomb = 1.2 ; Short-range electrostatic cut-off
vdwtype = Cut-off
vdw-modifier= force-switch
rvdw-switch = 1.0
rvdw = 1.2; Short-range Van der Waals cut-off
fourierspacing = 0.12
pme_order = 4
ewald_rtol =1e-09
epsilon_surface = 0
pbc = xyz ; Periodic Boundary Conditions
(yes/no)
nsteps = 1000
From: Smith, Micholas D.<mailto:smit...@ornl.gov>
Sent: woensdag 26 februari 2020 14:10
To: Katrien Clerx<mailto:katrien.cl...@student.kuleuven.be>;
gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>
Subject: Re: [gmx-users] Normal mode analysis
Hmmm
How did you prepare the structure? Also, attachments are stripped from emails
to the mailing list, can you please provide your mdp file as plain text in your
reply.
===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University o