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[ESPResSo] Fwd: Re: Visualisation of MD trajectories - assigning of angl


From: Marek Maly
Subject: [ESPResSo] Fwd: Re: Visualisation of MD trajectories - assigning of angle and dihedral parameters - rdf over more configs ?
Date: Tue, 06 Apr 2010 14:23:09 +0200
User-agent: Opera Mail/10.10 (Win32)


Hi Axel,

thanks a lot !

I was thinking that it will be probably like you wrote but
I just asked for sure to eventually save some time ...

Best,

     Marek



Dne Tue, 06 Apr 2010 10:33:39 +0200 Axel Arnold
<address@hidden> napsal/-a:

Hi!

On Tuesday 06 April 2010 00:48:36 Marek Maly wrote:
#2
Is in actual Espresso possible to set angle and dihedral parameters just
using
particle types of bonded particles similarly like in atomistic forcefields
are predefined these parameters
according to the atom types of the bonded triplet or quaternion of atoms ?

Let say that I have particles of type 0 and 1 in my system. It is possible
to define "globally" angle parameters
for all the relevant  combinations of bonded particle types:

0-0-0, 0-0-1, 0-1-0 , 1-0-1, 1-1-1 (for angle parameter setting)

or

0-0-0-0, 0-0-0-1 ... (for dihedral parameters)

No. Angular and dihedral potentials are only available as bonded potentials, which are specified on a per-particle basis. Of course, you can write a Tcl
procedure which checks the particle types and adds the necessary bonds.

#3
Is there available exmple of Espresso calculation where the

analyze <rdf>

command is used to calculate radial distribution function averaged over
previously stored configurations ?

Look into the "First steps" section of the Users' Guide. There is a small
tutorial, in which among other things the rdf is calculated. Whether
configurations were stored before or are generated on the fly doesn't matter,
if you read them back.

Is it really necessary to store configurations in files to calculate <rdf>.

It is not necessary to store the configurations, as I said above - whether
configurations are first stored and then read back, or are analyzed at
production, doesn't matter. In fact, the analzye rdf command works always on the internal particle coordinates of the integrator. Reading back for analysis
just means setting these internal coordinates.

I mean is it possible to calculate <rdf> during simulation from
let say last N loops of the INTEGRATE "for" cycle (of course without my
own tcl coding).

Without Tcl coding, Espresso won't do anything, so the answer is no. You will
need to write your own averaging, just as in the Users' guide.

Regards,
Axel



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