Force field for organic compounds

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1

Dear All,

I have a simulation which has an organic compound (C3H3N6). I have been reading literature to understand which force field would be apt and I believe I need to implement Polymer Consistent Force Field (not sure).

Can someone please help me with a starting point? This is the first time I am simulating an organic compound. I created the data file with bond information but am stuck at interaction definition.

Thanks a lot for your help!

J.

2

A literature search will answer this Q better than the mail list.

Steve

3

Hi,

You may take a look at this page:

http://lammps.sandia.gov/prepost.html

Some people use msi2lmp tool to apply PCFF on their structure.

4

Thanks for your inputs!

However, I do not have access to Material Studio which I believe is needed for msi2lmp tool. Is there any other way to generate the pcff force field for the structures?

5

Thanks for your inputs!

However, I do not have access to Material Studio which I believe is needed
for msi2lmp tool. Is there any other way to generate the pcff force field
for the structures?

​sure, you can create those manually or with the help of some scripting
tools. as steve already indicated, ​first you need to study the published
literature and need to learn whether the force field of your choice is
reasonably well applicable for the kind of compound and environment, that
you are willing to model (this is something you have to do yourself, the
mailing list cannot do that for you). from the publication(s) of the force
field of choice, you can then learn the "force field rules" for how to
build a suitable topology and assign atom types, partial charges, bonds,
bond types/parameters, angle types/parameters, dihedrals etc.

depending on the specifics of your compound/system, this is easy to do or
tedious, can be scripted/automated or must be done manually. typically, the
assingment for bonded interactions follow the bond topology and the
assigned atom types. atom types are assigned based on chemical nature.

in the case of msi2lmp, you can build the required files manually (or from
scripting) as well, but you need to manually assign atom types and build
the bond topology. msi2lmp will infer the rest.

at any rate, the core step is, that you look up the relevant publications
describing the force field and the rules and then study the LAMMPS
documentation for data files and then think about how to best get from
point A to point B. it is unlikely, that there is a tool, that will just
read your mind and then realize what you want to do, not even materials
studio can do that for you.

axel.

6

Thank you Dr Axel!

7

Hi.
I attempted to reply to this question using a different subject
header. In case you missed it, here is the link:

https://sourceforge.net/p/lammps/mailman/message/35700652/

cheers