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Re: [lammps-users] Problem with a simulation
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Re: [lammps-users] Problem with a simulation

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sun, 10 Sep 2017 12:06:32 -0400

On Sun, Sep 10, 2017 at 7:44 AM, A. M.M <alaa.murar@...24...> wrote:
بسم الله الرحمن الرحيم


I attached to you two file ( Configuration and Input ) for a simulation of biomolecule called  "G6 EDA-cored PAMAM Dendrimer".

I faced many problems when I run this simulation and I solved all of them, but now when I run this simulation and after the first step it print "temp = -nan and all of energies = -nan", and when I check the xyz output file it contains only the initial positions that I configured and all new positions are equal to -nan.

Could you help me for find the wrong in this simulation?

​please check your geometry. you have a whopping 438 (out of 510) redundant positions, leaving only 72 unique positions.
have you visualized your starting geometry? is it supposed to be "flat".

there are many more questionable choices. please explain:

- the size of your simulation cell. if you don't want your molecule to interact with its periodic images, why not simply use fixed or shrinkwrap boundaries?
- the choice of your cutoff for coul/debye. your choice of box dimension suggests, that you don't want interaction with periodic images, by this will call in *a lot* of those. this is also in contrast with your morse potential cutoff, which is not exactly on the long side at 9 \AA. 
- the choice of special bonds. the FENE potential usually expects a different choice.
- the reason for setting a dielectric constant != 1 *and* using the coul/debye pair style.
- the reason for using the nsq neighbor list build method over the default binning.


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Dr. Axel Kohlmeyer  akohlmey@...12...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.