[gmx-users] usage trjconv in membrane simulation
Catarina A. Carvalheda dos Santos
c.a.c.dossantos at dundee.ac.uk
Wed Feb 22 11:58:08 CET 2017
Maybe check this: http://www.gromacs.org/Documentation/Terminology/Perio
As described 'there is no magic "do what I want" recipe', so you'll have to
try different options till you find a sequence that works for you.
Mine is the following:
1) -pbc cluster (protein) --> chances are you don't need this step
2) -pbc mol -center
3) -pbc whole --> as Alex suggested
4) -fit rot+trans ---> C-alphas only
Again, this might not work in your case.
On 22 February 2017 at 08:02, Alex <nedomacho at gmail.com> wrote:
> Have you tried '-pbc whole'?
> 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
>> Best regards,
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Catarina A. Carvalheda
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK
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