[gmx-users] usage trjconv in membrane simulation

[Alex]

Have you tried '-pbc whole'?

Alex

On 2/22/2017 12:57 AM, Мижээ Батсайхан wrote:
> Dear gmx user,
>
> Hello, I complited calculation of KALP15 in DPPC. I would like to make
> further analysis such as generate structures  of trajectory.
> I used following sequence of commands for gmx trjconv:
>
> 1. -pbc nojump
> 2. -pbc mol -ur compact
> 3. -pbc res (one case, ignored, but result is same)
> 4. -fit transxy
>
> In the result, there are some atoms of water very far from the system.
> How can I get right structure view?
> Please advice me?
> Is there any common used sequence of trjconv's command this type of
> situation?
>
> Best regards,
> Mije