On Tue, 22 Jan 2008 08:39:04 +0000 (GMT)
Anirban Ghosh <[EMAIL PROTECTED]> wrote:
Hi Friends,
I am simulating a 463 aa protein in water only along the 1st Eigen Vector
i.e. I am trying to do Essential Dynamics along First Principle Component. I
have used the make_edi command to generate a .edi file and then using it to
run the mdrun. But my problem is that every time after a simulation of 5 nano
second, I am finding that the pretein is coming out ofthe water box,
partially. I am using VMD to view the dynamics after the simulation is
complete. Is it a problem with GROMACS or VMD or is it that since I am using
Periodic Boundary Condition, the portion of the protein which is looking to
be outside the box, is actually inside another adjacent box, partally? Is
there any way to rectify this or am I doing the correct thing? Please
suggest. Any suggestion is welcome. Thanks a lot.
This is due to the use of periodic boundary condition.
Actually the whole protein should go in and out of one side to the
other of the box! You might have used the -pbc inbox option in trjconv?
To fix it you can either:
1: trjconv -f input.xtc -o output.xtc -pbc nojump
this will remove the jumps of in/out of hte box and show the protein
diffusing freely in space.
2: trjconv -f input.xtc -o output.xtc -fit rot+trans -n index.ndx -o ref.gro
this will allow you to remove the translation and rotation of the protein
and place it on a reference fame using a set of atoms that you can
define in index.ndx. If the ref.gro is a conformation at the center of
the box ... then you got your trajectory with the protein at the center.
XAvier
Cheers,
Anirban Ghosh
M.Tech Bioinformatics
University of Hyderabad
Project Trainee
Centre For DNA Fingerprinting & Diagnostics (CDFD)
Hyderabad
India
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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