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Re: [lammps-users] Making data file with a hybrid force-field
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Re: [lammps-users] Making data file with a hybrid force-field


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Tue, 12 Dec 2017 14:28:06 -0500



On Tue, Dec 12, 2017 at 1:27 PM, Robert McAllen <mm229196@...7214...78...> wrote:
Dear all

I'm going to simulate a system comprised of diverse types of materials, such as crystal, protein, and ions. 

But, I found it really tremendous to make a data file for a huge system based on a hybrid force-field (for example a combination of ClayFF and OPLS).

I already tried topotool in vmd, but, it lacks such general ability.

​you can still generate a data file, but just leave out the force field information. it is the better approach anyway. ​just put your pair_coeff statements into the input file or put them into a separate file and use "include".
 
Is there any proper software or code for this task? 

​the biggest problem here is that what you are trying to do is not "proper" in the first place, but rather a crutch that people use, if they have no other, better options.​

​since this is specific to your choice of force fields, there is little use to try and generalize and automate that. this can be done for setups, where you use only a single force field, but if you are mix and matching multiple force field, the generation of the mixed term is ambiguous. so you'll first have to decide how to do this. you most certainly will have to generate and specify those mixed interactions explicitly. 

the easiest way to deal with this is to write a script/program that implements the "rules" that you decide on and then outputs the necessary LAMMPS commands so they can be captured in a file.
​this at least takes away the risk of typos and violations of the expected format. ​editing files that have to follow a specific format in a plain text editor is something that you don't want to do anyway, except for the simplest of cases. writing a script/tool/program to do this is almost always preferred.
 

I'm really curious to understand how others deal with such systems as claimed in the literature !!

​you should ask those people. that is why papers have "corresponding authors" (at least in theory, that is).

axel.​

 

Bests




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--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.