[gmx-users] usage trjconv in membrane simulation

[Marlon Sidore]

Hello,

I had success with membrane simulations with:

1) -pbc nojump
2) -center
3) -pbc mol
4) -fit rot+trans

This usually works to have the protein fitted and centered.

Best regards,

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2017-02-22 8:57 GMT+01:00 Мижээ Батсайхан <b.mijiddorj at gmail.com>:

> 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
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