[gmx-users] trjconv and -pbc

[lina]

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,

>
> Jan
>
> ===========================================================
> Jan Marzinek
> PhD Candidate
> Centre for Process Systems Engineering
> Department of Chemical Engineering
> Imperial College London
> South Kensington Campus
> London SW7 2AZ
> E: j.marzinek10 at imperial.ac.uk
> M: +44(0)7411 640 552
>
>
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