2013/9/17 Zhicheng <[email protected]>:
> 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
> 在 2013年9月17日星期二UTC+8下午9时41分06秒，Victor Rühle写道：
>>
>> 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 <[email protected]>
>>>
>>> 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.
>>>
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>>
>>
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--
Christoph Junghans
Web: http://www.compphys.de
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