I have a question regarding the simulations that I am running. I tried
creating a pdb file with one methane and water molecules, but the
system keeps showing 'bad contact' error when I run the minimization
step and I don't understand what I am doing wrong.
This is my methane file :
TITLE methane in water
CRYST1 33.010 33.010 33.010 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 CH4 CH4 1 19.520 25.090 16.410 1.00 0.00
So I use this file and run editconf -f methane1.pdb -o box.pdb -bt
cubic. This creates a
box with volume of around 35 nm^3
Then I add water molecules using :
genbox -cp box.pdb -cs spc216 -o methwa.pdb -p topol.top
This adds around 1191 water molecules to the existing methane file. So
my box is now
(33.010 33.010 33.010 with total 1192 molecules). Then I run
minimization on this system
using minim.mdp as follows:
integrator = steep
emtol = 1.0
nsteps = 100
nstenergy = 10
nstxtcout = 10
xtc_grps = CH4 SOL
energygrps = CH4 SOL
nstlist = 5
ns_type = simple
rlist = 1.0
coulombtype = cut-off
rcoulomb = 1.0
rvdw = 1.0
constraints = none
pbc = no
grompp -f minim.mdp -c methwa.pdb -p topol.top -v
mdrun -v
And it runs minimization with bad contact errors and this is the result I get:
Steepest Descents converged to machine precision in 32 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -4.9481789e+04
Maximum force = 3.2827865e+06 on atom 500
Norm of force = 6.9951227e+04
Any suggestions?
Nisha.P
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