I am using GROMACS 5.1.5, for MD simulation of a dimeric protein to study the gradual separation of two chains.
However, in certain frames (as seen in VMD) the chains are suddenly completely separated within an interval of 0.01 ns. (see video attached)
The separation is not supposed to be so sudden (43 Å to 108 Å within 0.01 ns).
The images of frames of 52.44 ns and 52.45 ns are attached.
Is this a glitch?
Please turn on your PBC in VMD and have look at the box. It seems you may need to centre your trajectory to get rid of the PBC issues or there are other options as well.
Dear Uddipta,
You should turn on the PBC and check the same in VMD. And you can also use trajectory conversion flag -trjconv.
Ioana Mariuca Ilie Kailash Jangid R C Dash Vishal Pandya
The PBC Correstion has already been done.
This visualization is prepared AFTER THE PBC CENTERING.
Also, the literature suggests that the closed and open forms are in equilibration.
Does the visual representation of the Equilibration look like this?
Hello, I am facing a similar issue and I am unable to address it, did you get to solve it?
@Sanjana Pandey, Instead of doing just a single step PBC Correction, I performed 3 steps of PBC
And it solved.
Correction.
gmx trjconv -s em.tpr -f polymer.xtc -o polymer.whole.xtc -pbc whole
gmx trjconv -s em.tpr -f polymer.whole.xtc -o polymer.whole.nojump.xtc -pbc nojump
gmx trjconv -s em.tpr -f polymer.whole.nojump.xtc -o polymer.whole.nojump.mol.xtc -pbc mol
Hope it'll help.
@Uddipta Ghosh Dastidar
Thankyou, did you by any chance removed the PBC correction and then correct by whole flag followed by -ur compact flag.
Also, did you try a bigger box?
@Sanjana Pandey
Initially I used "......... -center -pbc mol -ur compact"
then i found the mentioned error.
When i tried with the above 3 steps, instead of this single step, the problem was solved.
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