Hello Everyone，
I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot but
find little useful.
My Gromacs was installed in a Linux cluster.
Follows is my steps to do normal mode analysis:
• pdb2gmx -ignh -ff < forcefield > -f <protein.pdb> -o mut.gro -p topol.top
• editconf -f mut.gro -o box.gro -d 1.5
• grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
• mdrun -s em.tpr -deffnm em -c em.g96 -v
• grompp -f nm.mdp -c em.g96 -o nm.tpr
--------------->WARNING 1 [file nm.mdp]:
The switching range for PME-Switch should be 5% or
less, energy
conservation will be good anyhow, since ewald_rtol =
1e-05
I have taken advises from the forum that I should not genbox and should use
cg instead steep for em in order to do Normal Mode Analysis, but now I am
facing problem of PME-Switch.
Does anyone have any experience on this?
Thanks in advance.
Kevin
==============Attached is em.mdp and nm.mdp=========================
em.mdp
define = -DFLEXIBLE
constraints = none
integrator = cg
dt = 0.002 ; ps !
nsteps = 400
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
optimize_fft = yes
emtol = 1000
emstep = 0.01
---------------------------------------
nm.mdp
constraints = none
integrator = nm
dt = 0.002 ; ps !
nsteps = 400
nstlist = 10
ns_type = grid
rlist = 1.2
coulombtype = PME-Switch
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.4
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