Polymer with straight backbone

EMC
1

I want to make a polymer with straight backbone and perform the relaxation later. But using the example build.emc file, I always get polymer where monte carlo moves have already been applied and there is torsion in the backbone. Also, is there any way to start a polymer from certain coordinates?

2

Exactly which example build.emc are you using? You can force the first molecule or cluster at the origin by setting option build_center to true.

3

I generated the build.emc file by running the polymer.esh template file.

4

Which polymer.esh file? There are 9 of them in total in the examples directory. Let’s assume, you would like to generate a single strand of polyethylene in empty space. The example below is based on

$EMC_ROOT/examples/setup/polymer/homopolymer/polymer.esh

First, one needs to define the simulation conditions by setting options. This example uses PCFF as force field, sets a density 0.01 g/cc, sets a temperature of 1 K, and generates exactly one strand by using the number option, placing this strand in the center of the box by using the focus option,

ITEM	OPTIONS

replace		true
field		pcff
density		0.01
temperature	1
number		true
focus		true

ITEM	END

The choice of a temperature of 1 K promotes the formation of a straight backbone. Chemical definition follows simulation sizing. The build of polyethylene requires the definition of an ethyl repeat unit flanked by a methyl group as cap:

# Groups

ITEM	GROUPS

ethyl		*CC*, 1,ethyl:2
methyl		*C, 1,ethyl:1, 1,ethyl:2

ITEM	END

Connectivity needs to be defined since we are using repeat units to define the final polymer. Subsequently, we need to define the polymer molecule in the clusters paragraph,

# Clusters

ITEM	CLUSTERS

poly		alternate, 1

ITEM	END

where the number 1 warrants the formation of just one polymer strand. An alternate pattern is chosen for creation of a sequential output. Finally, the polymer structure itself needs to be defined in the polymers paragraph,

# Polymers

ITEM	POLYMERS

poly
100		ethyl, 10, methyl, 2

ITEM	END

Here a polymer with 10 ethyl units and 2 methyl end-caps is created. The resulting chain represents the most likely conformer. Note that this approach can also be used to generate conformers for quantum mechanical calculations.

1 Like
5

I use the same script, but in my case my mononer is CC([N+].[Cl-]) and terminator is *C. I used temperature 1K, but at some step it is taking forever. I used ntrials equal ranging from 1000 to 100000, but still it shows inadequate trials.
I also tried with 1.5K, 2K, but still I did not get a straight backbone.

6

Which force field are you using? I assume, that you are using a different force field than PCFF, since parameters for terminal ammonium groups are missing. Please note – as stated in my last remark – that the above produces conformers, since the process at the base of building in EMC is a Monte Carlo-based algorithm. Different chains are built depending on the torsional definitions of the force field.

7

You are right. I was not using pcff, rather using opls-aa. Thanks for your all helpful replies.