[gmx-users] protein has broken after 100ns simulation

[Dries Van Rompaey]

Hi,

The mailing list removes attachments. Your best bet is uploading your snapshot to an image sharing service.
Sometimes several uses of trjconv are required to fix pbc issues.


> On 02 Jul 2016, at 08:16, Seera Suryanarayana <palusoori at gmail.com> wrote:
> 
> Dear gromacs users,
> 
> I have simulated protein for 100ns. When I visualized the protein in VMD, I
> have seen the protein into different fragments. Later I came to know that
> there is no breaking phenomena in simulations and that is because of the
> PBC problems. I have executed the trjconv command with following arguments
> to solve the problem, but I couldn't make it successful. I also attached
> the snapshot. Kindly guide me how to resolve problem?
> 
> gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -center -pbc
> mol -ur compact
> 
> Surya
> Graduate student
> India.
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