[gmx-users] Radial distribution function for larger distances

[Justin Lemkul]

On 2/8/17 12:48 AM, Subashini .K wrote:
>
> Hi,
>
>
> Thank you for the reply.
>
>
> I got RDF for distances up to 1.772 angstrom (in x-axis) using the code mentioned.
>

GROMACS does not output anything in Angstrom, so be sure you understand the 
units you're seeing.  Also the "code" you showed before is an .mdp file and has 
nothing to do with RDF analysis.  If you want comments on doing an RDF 
calculation, you'll have to provide your actual gmx rdf command and any relevant 
output from it.

>
> Can we get it for 15 angstrom?
>

As per the help description, the RDF is computed up to half the box length with 
PBC and up to 3 times the box length without.

-Justin

>
> 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
>
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================