coarse-grained bead is bigger than half the box

[Zhicheng]

Hi:

    When I am mapping the polymer to coarse-grained bead, I get the following error message:

                      an error occurred: coarse-grained bead is bigger than half the box

 

What is wrong with this? How can I fix it? I am very appreciating for anyone's help.

[Victor Ruehle]

Dear Zhicheng,

votca does not fix if molecules are broken along pbc. You can use gromacs to do that:

trjconv -pbc mol ...

This is a sanity check, if your molecule is really bigger than half of the box AND you put the whole molecule into one bead, you m ight want to disable this check.
Also see here:
https://groups.google.com/forum/#!msg/votca/7qikLTcqu2M/coCq-zZYR9AJ

This currently requires tweaking the code, if you really need it let me know.

Best,
Victor

2013/9/17 Zhicheng <zcgu...@gmail.com>

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[Zhicheng]

Dear Victor

 

There are three types of beads(type A,B and C) in my simulation. I don't want to map the whole polymer molecule to one bead. I just map the VDF residue to type A bead, CTF residue to type B, FBG and FEN to type C. It means that there are 56 type A beads(A1,A2,……A56), 56 type B beads(B57,B58,……B112) and 2 type C beads(C1,C2) in coarse-grained model of polymer.
在 2013年9月17日星期二UTC+8下午9时41分06秒，Victor Rühle写道：

[Christoph Junghans]

2013/9/17 Zhicheng <zcgu...@gmail.com>:

> Dear Victor
>
> There are three types of beads(type A,B and C) in my simulation. I don't
> want to map the whole polymer molecule to one bead. I just map the VDF
> residue to type A bead, CTF residue to type B, FBG and FEN to type C. It
> means that there are 56 type A beads(A1,A2,……A56), 56 type B
> beads(B57,B58,……B112) and 2 type C beads(C1,C2) in coarse-grained model of
> polymer.

There is an mistake in your mapping file:

...
<cg_bead>
<name>B72</name>
<type>PCTFE</type>
<mapping>B</mapping>
<beads>72:CTF:C1 57:CTF:C2 72:CTF:F2 72:CTF:F1 72:CTF:F3
72:CTF:F4</beads>
</cg_bead>
..

atom 72:CTF:C1 and 57:CTF:C2 a really far apart! You need to change it
to 72:CTF:C2. This mistake is copy-pasted at least 20 times in
different cg beads.

Cheers,

Christoph

--
Christoph Junghans
Web: http://www.compphys.de