[gmx-users] About rlist, rvdw

[Justin Lemkul]

On 10/8/18 8:42 AM, 高恺 wrote:
> Dear gromacs users,
>
> I have recently done some simulations of CH4-Graphite desorption. I put methane into the graphite pores, and the pores are connected to the outside by a channel, allowing methane to spontaneously desorb because of the pressure difference and finally reach equilibrium.
> This is a simple simulation, but I noticed that using different rlist, rvdw values, the density of methane in the hole will be significantly different after the system is equilibrated.
> In my understanding, the larger the rlist/rvdw, the closer the simulation results are to the real world. But I don't understand why rlist/rvdw has such a big impact on simulation results. If the result of setting rlist=2 is significantly different from the result of setting rlist=1, does it mean that the result of setting rlist to 1 is not trusted?

The cutoffs used are a part of the force field. They're not something 
that can just be set arbitrarily. You need to use whatever settings are 
appropriate for the force field model you've chosen to employ and not 
deviate unless you can demonstrate your approach is more robust across a 
suitable test set of systems.

-Justin

> I am using following parameters (mdp file):
> ------------------------------------------------------
> ; Run parameters
> integrator                   = md
> nsteps                        = 20000000
> dt                               = 0.001
> comm-mode              = None
>
> ; Output control
> nstxout                  = 50000
> nstvout                  = 50000
> nstfout                   = 50000
> nstlog                    = 50000
> nstenergy               = 50000
> nstxtcout                = 1000
> xtc_precision           = 10000
> energygrps             = GRA GAS
>
> ; Neighborsearching
> ns_type                  = grid
> nstlist                     = 5
> rlist                         = 1
>
> ; VDW
> vdw-type                 = cut-off
> rvdw                         = 1
>
> ; OPTIONS FOR ELECTROSTATICS
> coulombtype              =cut-off
> rcoulomb                    = 1
>
> ; Periodic boundary conditions
> pbc                             = xyz
>
> ; TEMPERATURE COUPLING
> Tcoupl                   = nose-hoover
> tc_grps                  = GRA GAS
> tau_t                      = 2 2
> ref_t                       = 400 400
>
> ; VELOCITIES GENERATION
> gen_vel                     = yes
> gen_temp                 = 400
> gen_seed                  = 391482
>
> ; ENERGY GROUP EXCLUSIONS
> energygrp_excl           = GRA GRA
>
> ; Other Settings
> freezegrps               = GRA
> freezedim                = Y Y Y
> -------------------------------------------------------------------
>
> I would be very grateful if anyone can help me.
>
> Kevin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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