[gmx-users] Normal Mode Analysis with Gromacs 4.6

[mcfc1301]

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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