[gmx-users] usage trjconv in membrane simulation

Мижээ Батсайхан b.mijiddorj at gmail.com
Wed Feb 22 08:57:28 CET 2017

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

Best regards,

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