Hello,
I need to build a polymer molecule for my molecular dynamics simulation. The target molecule is a random polymer composed of two monomers randomly connected with each other. I know Materials Studio could build random polymer, but is there any other good packages could do the same task? If there is any, could you please recommend that to me?
Any help would be much appreciated!
Hi
If your monomers aren't in the data bank and you can't import monomers from software, you should draw the monomer structure and use repeating unit in the build section, then determine the head and tail atom of your structure. After that, going to build random copolymer, then in the section of selecting structures, choose current project and your drawn structure.
If my explanation isn't clear, you can answer me.
You can use Enhanced Monte Carlo (EMC), by Pieter in 't Veld.
https://montecarlo.sourceforge.net/emc/Features.html
You can construct alternate, block and random co-polymers.
Hello Parastoo Ahmadpour-Samani,
Thank you very much for your reply!
I think your reply is about how to use Materials Studio to build the random polymers. A lot of people are using that, but I am not sure whether it is reliable. So I am trying to find another alternatives if there is any existing.
Hello Israel Zadok ,
Thank you very much for your recommendation!
That looks very good. The software seems to be under active development too.
Could you please tell me whether the software are widely been used and has been kind of be demonstrated to be very reliable?
Thanks in advance!
Well, it is not as widely used as material studio.
But for a package developed by a single person, it is very functional, flexible and capable.
It is text based, but with a few lines of simple parameters and smiles, you can build very complex systems.
Learning curve is steep at first, but there are many examples supplied with the code.
Hello Israel Zadok ,
Thanks very much for the reply!
Since it is only command based software, as you said, it has a steep learning curve. You have lots of experience, if you do not mind, may I ask you a specific question? If the software is not able to build the polymer I need, I will skip trying to learn it.
The polymer I would like to build is glucomannan (https://www.wikiwand.com/en/Glucomannan), two kinds of monomers (mannose and glucose) connect with each other with beta-(1-4) linkage. The ratio of the two monomers will be assigned, but the sequence will be random. If it is possible, branching may also need to be introduced. Do you think Enhanced Monte Carlo could do this? For your quick reference, a schematic figure of the chemical structure can be found here. Article Nutritional and Potential Health Benefits of Konjac Glucoman...
Any help would be much appreciated!
Here is an example script for a random co-polymer from EMC
As you can see, you specify the force-field, number of atoms, monomers using SMILES. connectivity * options for the monomers. You need terminal chemistry, methyl in this case. You specify clusters, only polymer in this case. Then the co-polymer composition, a ration of 1:3 ethyl to propyl, 6 monomer units and 2 terminal methyl units.
change the force-field, add your monomers and terminals in smiles, and your desired polymer composition and length.
You can also add water, to the groups and the clusters, to solvate the system.
----------------------------------
ITEM OPTIONS
field opls-ua
ntotal 5000
mass true
replace true
ITEM END
# Groups
ITEM GROUPS
ethyl *CC*,1,ethyl:2,1,propyl:2
propyl *CC(C)*,1,propyl:2,1,ethyl:2
methyl *C,1,ethyl:1,1,ethyl:2,1,propyl:1,1,propyl:2
ITEM END
# Clusters
ITEM CLUSTERS
poly random 100
ITEM END
# Polymers
ITEM POLYMERS
poly
100 ethyl:propyl=1:3,6,methyl,2
ITEM END
---------------------------------------------------------
Hello Israel Zadok ,
Thank you very much of the very detailed answers!
Sorry for the later reply.
According to the example in your reply, it looks really great.
Thanks for the recommendation, I will give a it a try.
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