[gmx-users] usage trjconv in membrane simulation

[Catarina A. Carvalheda dos Santos]

Hi Mije,

Maybe check this: http://www.gromacs.org/Documentation/Terminology/Perio
dic_Boundary_Conditions?highlight=trjconv

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.

Good luck.



On 22 February 2017 at 08:02, Alex <nedomacho at gmail.com> wrote:

> 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
>>
>
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-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK