[gmx-users] Normal Mode Analysis with Gromacs 4.6

[Mark Abraham]

Why are you using PME-switch? Without explicitly choosing a switch?

Mark


On Thu, Dec 12, 2013 at 6:45 PM, mcfc1301 <mcfc1301 at gmail.com> wrote:

> 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
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Normal-Mode-Analysis-with-Gromacs-4-6-tp5013240p5013276.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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