[gmx-users] Change PBC box size after simulation.

[Max Adamyan]

Thank you for your response. Yes my input to `trjconv -s` has my system in such way that I can make all my desired calculations (as far as I can see in VMD).

Sincerely
       Max.

> On Jan 25, 2019, at 22:11, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 
> Hi,
> 
> What property do you want to make true? Does your input to trjconv -s have
> it?
> 
> Mark
> 
>> On Fri., 25 Jan. 2019, 10:37 Max Adamyan, <max.adamyan at gmail.com> wrote:
>> 
>> Hi. After simulation, I have trajectory file with broken and jumping atoms.
>> I've fixed broken atoms, and some of jumping, but no-meter how hard I try,
>> I cannot get rid of all of it. I've read Gromacs suggested workflow
>> <
>> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>>> 
>> to
>> fix it like 100 times. I've tried literally every `gmx trjconv` options
>> (and chains of options), with no success. At this point I think that my
>> System is transforming in such way, that it just cannot fit inside PBC box.
>> Can this be the case? If so, can I make my PBC box bigger in z direction?
>> Or maybe there is some other way to fix it?
>> 
>> --
>> Sincerely,
>>    Max Adamyan
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