[gmx-users] About g_sdf in version 4.6.5.

[Dallas Warren]

That is correct.

(whoever is Darren? ;) )

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Tue, 16 Jul 2019 at 16:32, Henry Vider <henry.vider at ut.ee> wrote:

> Darren, so generating SDF over several molecules is possible with the
> version you mentioned?
>
> Sincerely,
> Henry
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Dallas
> Warren <dallas.warren at monash.edu>
> Sent: Tuesday, July 16, 2019 12:30:19 AM
> To: GROMACS users
> Subject: Re: [gmx-users] About g_sdf in version 4.6.5.
>
> Yes, it is still only summing over a single molecule since version 5 I
> think, don't know exactly when the change occurred. Last version I have
> used (and still use) for generating SDFs is 4.0.7
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On Tue, 16 Jul 2019 at 01:43, Henry Vider <henry.vider at ut.ee> wrote:
>
> > Dear all,
> >
> > I have a system consisting of 10 solute molecules and two different
> > solvents. When generating Radial Distribution Functions and selecting the
> > solute molecule for reference, I get RDFs averaged over 10 solute
> > molecules. However, when generating SDF .cube file, results cannot be
> > properly visualized in VMD for some reason. This is not the issue when I
> > have systems consisting of 1 solute molecule and generate .cube files for
> > these systems.
> >
> > I read in mailing list archives that SDF function does not average over
> > several reference particles after version 3.x something. Is this still
> true
> > with even newer versions, and also in 4.6.5?
> >
> > Sincerely
> > Henry
> > --
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