[gmx-users] polymer in octahedron box pbc problem

[gromacs query]

Hi,

I think its solved, I used -center option but now rather selecting full
polymer I selected some of the central residue in polymer chain. Now box
looks good and polymer is not broken.

JIom

On Thu, Oct 1, 2015 at 3:43 PM, gromacs query <gromacsquery at gmail.com>
wrote:

> Hi Victor,
>
> With 'pbc whole' polymer remains broken in pbc and the octahedron box
> looks weird too.
>
> JIom
>
> On Thu, Oct 1, 2015 at 2:52 PM, Victor Rosas Garcia <
> rosas.victor at gmail.com> wrote:
>
>> Have you tried the option "-pbc whole" instead of "-pbc mol"?
>>
>> Victor
>>
>> 2015-10-01 6:43 GMT-05:00 gromacs query <gromacsquery at gmail.com>:
>>
>> > Hi All,
>> >
>> > I have linear polymer in octahedron box and when I try to visualise a
>> > polymer in octahedraon box then water octahedron box looks as expected
>> but
>> > my polymer looks broken.
>> >
>> > trjconv_avx -f input.xtc -o out.xtc -pbc mol -ur compact  -s input.tpr
>> -b
>> > 100000
>> >
>> > I have tried to use -center (whole polymer selection) also but still it
>> > looks broken.
>> >
>> > I want to write some pdbs for some analysis and this way my polymer is
>> > broken in pbc.
>> >
>> > Thanks for any suggestions.
>> > JIom
>> > --
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