Construction of a Bead-Spring Polymer Model for LAMMPS

This exercise is intended for construction of oarse-grained (bead-spring) molecular dynamics models of a collection of polymer chains with sizeable monomeric groups connected by ethylene linkers in either E or Z conformation. An example is the following polynorbornene-like system:

E linkmonomerZ link
where the first structure is an E-ethylene linker, the second is your monomer, and the third is a Z-ethylene linker. Any solvent molecule of your choice may also be incorporated in your system.

1) build and save short segments of your polymer containing:

    E - MON - E - MON
    Z - MON - Z - MON
    E - MON - Z - MON

   Terminate the segments with the appropriate H's, but remember which H's
   were added, since you will need to delete these 2 H's again in step 4)

2) Use InsightII to convert each of these structures to CHARMM format and
   run CHARMM minimizations on them (do not add charges either in SYBYL or
   in CHARMM).

3) Convert the optimized structures back to mol2 format and for each segment in
   turn, do the following 6 steps:

4) Load the structure into SYBYL, delete the two terminal H's and extract each
   of the four monomers into a separate molecular area

5) For each monomer from step 4), generate a mass centroid via the following
   command (e.g., for a monomer in M2):


6) Merge the constituent monomers (with mass centroids) back into a single
   molecular area and save with a distinct name.

7) Reconnect the monomers:  Build/Edit  >>  Add  >>  Quickbonds...  >>  {all}

8) For the optimized structure, measure and record each of the following
   parameters:  R(Z-M), R(M-Z), A(Z-M-Z), A(M-Z-M), T(Z-M-Z-M)
   where each parameter is defined with respect to the center of mass.

9) Increase by 0.10A the bond distance between the C.2 on Z that connects to
   the C.3 on M.  Then increase the bond distance on the other side of the
   monomer (the C.3 on M that connects to the C.2 on Z) by the same amount.
   Remeasure R(Z-M) and R(M-Z) and record their new values.

10) Repeat 9) again, except this time decrease the bond distances by 0.10A
    relative to the original values, and record the new values.

11) From the unmodified structure (i.e., before step 9) increase the angles
    formed across the C=C chain bond to the monomer (i.e., from C.2 on the
    connector to C.2 on the connector to C.3 on the monomer) by 10 degrees,
    then remeasure A(Z-M-Z), A(M-Z-M).

    Note -- the angles you must modify include each of the following:

          M - Z=Z - M - Z=Z
      1)            <------
      2)      ------>
      3)  <------

    Please be sure to enter the atoms into SYBYL's Analyze  >>  Measure
    utility in the order shown.

12) Do 11) again, except this time decrease each angle by 10 degrees relative
    to the original value.  Again record the values for A(Z-M-Z), A(M-Z-M).

13) From the unmodified structure, locate the torsion connecting the middle
    C=C connector to the middle monomer, i.e., the H - C.2 - C.3 - H torsion

       M - Z=Z - M - Z=Z

    then increase the value by 10 degrees and record the new T(Z-M-Z-M) value.

14) Repeat 13), except now increase this angle by 10 degrees relative to the
    original structure.  Rerecord T(Z-M-Z-M).

15) Construct a file which tabulates the data acquired in steps 8-14.  It
    should contain 6 lines and be in the following form:

RZM     4.725   4.819   4.912  
RMZ     3.888   3.959   4.030
AZMZ   85.61   85.40   85.23
AMZM   90.72  104.97  117.91
TZMZM 117.5   125.6   133.2

    Where the first line indicates which segment you're currently describing,
    the first column is a label indicating the parameter being measured
    (use REM,RME,AEME,AMEM,TEMEM for the EMEM segment, and RZM,RME,AZME,AMEM,
    TZMEM for the ZMEM segment), the second column contains the values
    corresponding to when you reduced the values of the structural parameters,
    the third column are the original parameter values, and the fourth column
    contains the values you got when you increased the values.  Note that the
    trends you get for angles between mass centroids are sometimes opposite the
    ones you had for the actual atomic angles.

16) Redo steps 8-15 for the other two segments, and append the results to the
    file created in step 15 (the final file should have 18 lines).

17) Create files for your monomer, your linker and your solvent molecule.  Note
    that you are going to use InsightII to create charmm input files for these
    files and InsightII balks when ethylene isn't fully protonated, so make
    your ethylene linker fully protonated.

18) Use InsightII to create monomer.crd, monomer.rtf, solvent.crd, solvent.rtf,
    E.crd and E.rtf files.  The fully protonated linker is equally applicable
    for either E or Z, so you can just copy the E.crd and E.rtf files to Z.crd
    and Z.rtf.

19) Edit E.crd and Z.crd to remove the H's you don't want.

20) Collect all of the *.crd and *.rtf files into once directory.  Also include
    the file with all of the geometry specification data that you collected in
    steps 8-16 -- call this file "geometry.spec".

21) Execute the command "beadset"

22) Answer the relevant questions asking for a random seed (must be an integer;
    may be any length), followed by questions regardind the size and
    composition of your polymer.

23) Once the program has finished, it will provide you with a file called
    "", which should be a valid LAMMPS data file.

David Johnson
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