[gmx-users] Re: A note while running grompp for nvt equilibration

[Dr. Vitaly Chaban]

> I am tyring to do a simulation of a monomer and an octamer of the same
> molecule
> using gromacs 4.5.3 with opls force field. Monomer simulations ran with out
> any note or
> warning, but when i tried to do nvt equilibration for the octamer, i got the
> following note while running grompp
>
> "NOTE 1 [file nvt.mdp]:
>   The sum of the two largest charge group radii (0.779095) is larger than
>   rlist (1.400000) - rvdw (1.000000)"
> The mdp file used is as follows:
>
> define                  = -DPOSRES
> integrator              = md
> dt                      = 0.002
> nsteps                  = 50000
> nstcomm                 = 10
> nstxout                 = 100
> nstvout                 = 100
> nstlog                  = 100
> nstenergy               = 100
> nstlist                 = 5
> ns_type                 = grid
> pbc                     = xyz
> rlist                   = 1.4
> coulombtype             = PME
> rcoulomb                = 1.4
> epsilon_r               = 1
> vdwtype                 = Switch
> rvdw_switch             = 0.9
> rvdw                    = 1.00
> fourierspacing          = 0.12
> pme_order               = 4
> ewald_rtol              = 1e-5
> optimize_fft            = yes
> Tcoupl                  = nose_hoover
> tc_grps                 = Protein  Non-Protein
> tau_t                   = 0.4      0.4
> ref_t                   = 300      300
> nh-chain-length         = 1
> pcoupl                  = no
> gen_vel                 = yes
> gen_temp                = 300.0
> gen_seed                = 1984
> continuation             = no
> constraints              = all-bonds
> constraint-algorithm     = LINCS
> lincs-order              = 4
> lincs-iter               = 1
> lincs-warnangle          = 30
>
>
> Can anybody please help me on how to go about with it?


1) Increase RLIST
2) Re-distribute atoms among charge groups so that to make charge
groups [spatially] smaller.



Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark