Generating the same random chain

EMC
1

Hello,

I’d like to generate a polymer melt consisting of a random copolymer. But I want all the chains to have the same microstructure. Reading the docs did not help but I may have missed a point. Is there any way to do that ?

Here is my input :

#!/usr/bin/env emc_setup.pl

# Options

ITEM		OPTIONS
field_debug reduced
replace		true
# mass		true
# ntotal	1
density		0.7
number          true
field		opls-aa
build_dir	.

ITEM		END

# Groups

ITEM		GROUPS

CBM         *C/C=C\C*, &
        1,CBM:2,  1,TBM:2,  1,VBM:2,  1,STM:2,  1,HT:1, &
        2,CBM:1,  2,TBM:1,  2,VBM:1,  2,STM:1,  2,HT:1

TBM         *C/C=C/C*, &
        1,CBM:2,  1,TBM:2,  1,VBM:2,  1,STM:2,  1,HT:1, &
        2,CBM:1,  2,TBM:1,  2,VBM:1,  2,STM:1,  2,HT:1

VBM         *C(C*)C=C, &
        1,CBM:2,  1,TBM:2,  1,VBM:2,  1,STM:2,  1,HT:1, &
        2,CBM:1,  2,TBM:1,  2,VBM:1,  2,STM:1,  2,HT:1

STM         *CC(C1=CC=CC=C1)*, &
        1,CBM:2,  1,TBM:2,  1,VBM:2,  1,STM:2,  1,HT:1, &
        2,CBM:1,  2,TBM:1,  2,VBM:1,  2,STM:1,  2,HT:1

HT          *H

ITEM		END

# Clusters

ITEM		CLUSTERS

poly		random	1

ITEM		END

# Polymers

ITEM	POLYMERS

poly
1		CBM,10,TBM,10,VBM,10,STM,10,HT,2

ITEM	END
2

Dear user,

To understand you correctly: you have a random copolymer of CBM, TBM, VBM, and STM, for which no predefined pattern is set and you strive for n exact copies?

If this is the case, you are aiming for a pseudo-random result, which would mean, that the user has to define the randomness of one chain. You can do this by using the alternate instead of the random cluster option. This allows you to define an exact sequence in your ITEM POLYMERS section, e.g.

# Clusters

ITEM	CLUSTERS

poly	alternate, 20

ITEM	END

# Polymers

ITEM	POLYMERS

poly
1		CBM,2,TBM,1,CBM,1,VBM,2,STM,1,...,HT,2

ITEM	END

where ... means that you would have to complete the sequence such, that your boundary condition of having a total of 10 CBM, TBM, VBM, and STM repeat units. The sequence would start with

[HT][CBM][CBM][TBM][CBM][VBM][VBM][STM][...][HT]

where [HT] is added as terminator. Please note that EMC can be finicky with respect to partial charge designation when using a single hydrogen as terminator.

The above would generate 20 clusters with the exact same sequence, since you set number to true under ITEM OPTIONS.

3

Dear veld,

Thanks for your reply, that’s exactly what I was thinking. Terminal H are not a problem, as I parse output pdb to use it for Gromacs. But I will keep that in mind in case of using with LAMMPS.

Thank you again !

4

Dear veld,

I noticed a strange behaviour. The attached input

#!/usr/bin/env emc_setup.pl

# Options

ITEM		OPTIONS
field_debug     reduced
replace		true
density		0.7
number          true
field		opls-aa
build_dir	.

ITEM		END

# Groups

ITEM		GROUPS

CBM         *C/C=C\C*, &
        1,CBM:2,  1,TBM:2,  1,VBM:2,  1,STM:2,  1,HT:1, &
        2,CBM:1,  2,TBM:1,  2,VBM:1,  2,STM:1,  2,HT:1

TBM         *C/C=C/C*, &
        1,CBM:2,  1,TBM:2,  1,VBM:2,  1,STM:2,  1,HT:1, &
        2,CBM:1,  2,TBM:1,  2,VBM:1,  2,STM:1,  2,HT:1

VBM         *CC(*)C=C, &
        1,CBM:2,  1,TBM:2,  1,VBM:2,  1,STM:2,  1,HT:1, &
        2,CBM:1,  2,TBM:1,  2,VBM:1,  2,STM:1,  2,HT:1

STM         *CC(C1=CC=CC=C1)*, &
        1,CBM:2,  1,TBM:2,  1,VBM:2,  1,STM:2,  1,HT:1, &
        2,CBM:1,  2,TBM:1,  2,VBM:1,  2,STM:1,  2,HT:1

HT          *H

ITEM		END

# Clusters

ITEM		CLUSTERS

poly		alternate	1

ITEM		END

# Polymers

ITEM	POLYMERS

poly
1    CBM,1,TBM,1,STM,1,CBM,1,STM,1,CBM,1,VBM,1,CBM,1,STM,2,TBM,1,VBM,1,TBM,1,CBM,1,STM,1,TBM,1,CBM,1,TBM,2,CBM,1,STM,1,VBM,1,STM,2,TBM,1,CBM,1,VBM,1,CBM,1,STM,1,TBM,1,VBM,2,TBM,2,STM,1,TBM,1,CBM,1,VBM,2,STM,2,CBM,1,VBM,1,CBM,1,VBM,1,STM,1,VBM,1,CBM,1,TBM,2,STM,1,TBM,1,STM,3,CBM,1,TBM,1,STM,1,TBM,1,VBM,1,STM,1,TBM,1,VBM,1,STM,1,VBM,1,TBM,1,STM,1,CBM,1,TBM,3,STM,1,CBM,2,TBM,2,STM,3,CBM,2,TBM,2,STM,1,TBM,1,CBM,1,TBM,1,CBM,3,STM,1,CBM,1,STM,1,VBM,1,CBM,1,VBM,1,TBM,1,VBM,1,STM,2,TBM,1,CBM,1,TBM,3,VBM,1,CBM,1,TBM,1,VBM,1,TBM,1,VBM,1,TBM,1,STM,1,VBM,1,TBM,3,CBM,1,VBM,1,CBM,1,VBM,1,STM,1,CBM,1,STM,2,CBM,1,VBM,2,TBM,1,VBM,4,STM,2,VBM,1,CBM,1,TBM,1,VBM,1,CBM,1,TBM,1,CBM,1,VBM,1,TBM,1,CBM,1,TBM,1,STM,1,TBM,1,STM,1,CBM,1,VBM,3,STM,1,CBM,1,TBM,1,VBM,2,CBM,1,VBM,2,CBM,1,STM,1,VBM,1,CBM,2,TBM,1,VBM,1,CBM,1,STM,1,CBM,1,TBM,1,VBM,1,STM,1,CBM,3,VBM,1,STM,1,CBM,2,STM,1,VBM,4,STM,2,CBM,1,VBM,1,STM,1,VBM,1,TBM,2,STM,1,VBM,1,TBM,1,STM,2,CBM,1,HT,2

ITEM	END

produces a pdb (attached) where repeat units are in different order.

Do you have any explaination ?

system.pdb (177.8 KB)