|From:||Axel Kohlmeyer <akohlmey@...24...>|
|Date:||Sun, 10 Sep 2017 16:50:35 -0400|
بسم الله الرحمن الرحيمHello,First, please see the attached article (especially the part of the Dendrimer model and simulation).
Second, the geometry should be a 3-D shape as in the article.
The article method has no simulation boundaries, so no periodic bc, but I chose this as a test.
The coul/debye potential in the article has no cutoff radius, so I chose this cutoff which is equal to the length of the box of simulation.
As for morse potential I chose the same cutoff as in the article. I chose lj/coul 1.0 1.0 1.0 for special bond because I need to calculate all interaction as in this article.
I chose the dielectric constant of the water which is the implicit solvent and coul/debye for pair style as in the article.
The choice of nsq came from a problem faced and this choice solved it, but I made some changes so I think the default one will work fine now. (I forgot return it to default one).
I hope that I help you guess the situation.
2017-09-10 19:06 GMT+03:00 Axel Kohlmeyer <akohlmey@...24...>:On Sun, Sep 10, 2017 at 7:44 AM, A. M.M <alaa.murar@...24...> wrote:بسم الله الرحمن الرحيمHello,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.axel.
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