[gmx-users] trjconv and -pbc

[Mark Abraham]

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).

Mark