[gmx-users] -pbc nojump failure

[Irem Altan]

Hi,

Thanks for your suggestion. Unsurprisingly, the structure in nvt_water_frozen.tpr is also fragmented. Is there a way to use the input .pdb file as reference, somehow?

Best,
Irem

> On Mar 31, 2016, at 12:45 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 
> Hi Irem,
> 
> Check the structure in nvt_water_frozen.tpr:
> 
> gmx editconf -f nvt_water_frozen.tpr -o ref.pdb
> 
> Cheers,
> 
> Tsjerk
> On Mar 31, 2016 00:04, "Irem Altan" <irem.altan at duke.edu> wrote:
> 
>> Hi,
>> 
>> I am simulating a protein in its unit cell. I use the original .pdb file
>> as an input, so the initial molecule is not fragmented. At the end of the
>> simulation, I generate a .pdb file containing the trajectory of the protein
>> as follows:
>> 
>> gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc
>> nojump -o prot.pdb
>> 
>> Despite the fact that I use -pbc nojump, I still get all the coordinates
>> wrapped into the unit cell, and therefore the protein fragmented. What
>> could be wrong? (I use GROMACS 5.1.2)
>> 
>> Best,
>> Irem
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