On the Construction of Polymers Comprising Three or More Monomers Using EMC

EMC
1

Hello everyone, I encountered the following error while attempting to construct a polymer with three or more monomers using EMC. Could anyone advise on the possible reasons for this issue?

Error: core/script/clusters/polymer.c:1036 ScriptClustersPolymerInit:
       Exceeded iterations for polymer 'poly'.
       Program aborted.

Here is my input file：

ITEM    OPTIONS

replace         true
field           pcff
ntotal          500

ITEM    END

# Groups

ITEM    GROUPS

A       *CNC*,1,B:1,2,B:1
B       *CC*,2,C:1
C       *CC(=O)C*,2,D:1
D       *CN

ITEM    END

# Clusters

ITEM    CLUSTERS

poly    random  1

ITEM    END

# Polymers

ITEM    POLYMERS

poly
1       A,1,B,2,C,2,D,2

ITEM    END
2

Dear user,

The error indicates an ill-defined polymer, i.e. your connectivity is inconsistent. The program tries to connect your groups through in iterative scheme, but can’t. Was jumps out at me, is that your polymer does not connect back from C to A. Your polymer definition also does not represent a classical definition of a random copolymer, but more a block copolymer, which also results in an impossible polymer definition when not all number of repeat units are the same. In your case, n_A != n_B. Creating a demonstrator using your example above, a correct random copolymer definition would be:

# Options section

ITEM	OPTIONS

replace		true
field		pcff
number		true
density		0.1
focus		true
emc_execute	true

ITEM	END	# OPTIONS

# Groups section

ITEM	GROUPS

A		*CNC*, &
		2, A:1, &
		2, B:1, &
		2, C:1, &
		1, D:1,2,D:1

B		*CC*, &
		2, A:1, &
		2, B:1, &
		2, C:1, &
		1, D:1, 2, D:1

C		*CC(=O)C*, &
		2, A:1, &
		2, B:1, &
		2, C:1, &
		1, D:1, 2, D:1

D		*CN

ITEM	END	# GROUPS

# Clusters section

ITEM	CLUSTERS

polymer		random, 1

ITEM	END	# CLUSTERS

# Polymers section

ITEM	POLYMERS

polymer
1		A, 1, B, 2, C, 2, D, 2

ITEM	END	# POLYMERS

In the above example all monomers are connected with all monomers and all monomers have a defined terminators for all connections. The above script can be downloaded here:

setup.esh (729 Bytes)

Other polymer architectures are possible too, assuming you define your connectivity correctly.

3

Thank you for your replying,I’m going to try this.

4

Meanwhile, I would like to construct a dendrimer molecule as shown in the figure. Could this be achieved in EMC?

picture
picture1920×1129 110 KB