[gmx-users] trjconv and -pbc

[lina]

On Fri, Oct 28, 2011 at 11:47 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 28/10/2011 2:39 PM, lina wrote:
>>
>> On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan
>> <j.marzinek10 at imperial.ac.uk>  wrote:
>>>
>>> ________________________________________
>>> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
>>> behalf of lina [lina.lastname at gmail.com]
>>> Sent: Thursday, October 27, 2011 10:47 AM
>>> To: Discussion list for GROMACS users
>>> Subject: [gmx-users] trjconv and -pbc
>>>
>>> Hi,
>>>
>>> I have a problem using
>>>
>>> trjconv_g -pbc nojump
>>> or
>>>
>>> trjconv_g -pbc nojump -center
>>>
>>> I even tried the -pbc whole.
>>>
>>> The system is protein with a small molecular, for the first time
>>> period, when I checked on pymol.
>>> they are together, but later they apart, after show cell, protein
>>> inside the cell, while this small molecular outside,
>>>
>>> I did not meet such issue before, it's used  to be easy to fix the pbc
>>> problem, but not this one. a bit surprise,
>>>
>>> They are supposed to be together,
>>>
>>> Thanks for any advice,
>>>
>>>
>>>
>>> I am sure it will help. Follow the workflow!
>>>
>>>
>>> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions?highlight=pbc
>>>
>>> Just use the trjconv -h to see each option.
>>
>> Ha, I think I have tried those options. That's why I am confused.
>>
>> Thanks,
>
> Well, you need to try them better :) If you want your trajectory to keep
> protein and something else together, you will need an index group that
> combines them not jumping, and then combines them centering (or whatever).

Thanks. I did use the index group on trjconv to output the pdb of the
protein and the small molecular.

>
> Mark
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