[gmx-users] Radial distribution function for larger distances

[Subashini .K]

Hi,


Thank you for the reply.


I got RDF for distances up to 1.772 angstrom (in x-axis) using the code mentioned.


Can we get it for 15 angstrom?


What should be done?


Thanks,

Subashini.K


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Christopher Neale <chris.neale at alum.utoronto.ca>
Sent: Wednesday, February 8, 2017 10:44 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Radial distribution function for larger distances

It's unclear what your issue is. I presume you are concerned that the rdf might not be valid at distances longer than your cutoff? In that case, adding dispersion correction might be something to think about, but then again that will depend on the force field and the system too. Unless I'm missing something you'll likely need to describe precisely what your problem is to get any useful suggestions.
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Subashini .K <subashinik at hotmail.com>
Sent: 08 February 2017 00:08:57
To: gmx-users at gromacs.org
Subject: [gmx-users] Radial distribution function for larger distances

Hi Gromacs users,


How to calculate RDF for larger distances, say 15 angstrom using the following code. In which line should we focus to make changes?


Can someone help?


integrator               = md
dt                       = 0.002     ; 2 fs
nsteps                   = 5000000   ; 10.0 ns

nstenergy                = 5000
nstlog                   = 5000
nstxout-compressed       = 2000

continuation             = yes
constraint-algorithm     = lincs
constraints              = h-bonds

cutoff-scheme            = Verlet

coulombtype              = PME
rcoulomb                 = 1.0

vdwtype                  = Cut-off
rvdw                     = 1.0
DispCorr                 = EnerPres

tcoupl                   = Nose-Hoover
tc-grps                  = System
tau-t                    = 2.0
ref-t                    = 298.15
nhchainlength            = 1

pcoupl                   = Parrinello-Rahman
tau_p                    = 2.0
compressibility          = 4.46e-5
ref_p                    = 1.0

Thanks,
Subashini.K