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

[Anu Chandran]

Sir,
Thank you for the reply. As per the suggestion, I tried increasing the
rlist. Note or warning stopped when rlist was increased to 1.8. Also with
this value of rcoulomb, the box size also needs to be increased. I would
like to know whether it is fine to keep rlist 1.8 and also whether there is
any other alternative rather than increasing rlist since increase in rlist
requires an increase in box size.
Thank you,
with regards
Anu

On Fri, Feb 15, 2013 at 5:28 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:

> > 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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>