Hi Ann,
I run a NPT simulation for 500 picosecond and when i see the output (.gro)
file in vmd i found some holes my simulation box.
I mean 2 or 3 chains were away from the center position of the box where
other chains were residing.
so i thought of performing a NVT simulation follwed by BD for my system to
be equillibriated.
1. Will that help in the purpose of equillibriation?
No. This has nothing to do with equilibration but is due to periodic
boundary conditions. Check chapter 3 of the manual, the wiki and the
archives of this list to learn more.
so, for that i wanted to center all the polymer chains inside the box and
performed the trjconv program.
But I wonder
2.Which ouput file from my 500 ps simulation (.xtc or .gro ) shall i use to
perform the trjconv and which options (-pbc nojump, -pbc whole) shall I
specify inorder to achieve my goal?
or
For centering you don't need any if the -pbc options. But when using
-pbc nojump you have to make sure that the reference structure is
close to the initial structure in the trajectory you want to reset, as
I explained in more detail last week or the week before.
3.the holes that i have mentioned before are accpetable or not?
Not a problem... PBC.
4.is it can be the problem with VMD visualisation?
Since it's not a problem it can't be a problem with visualization ;)
(Though it can pose a problem when visualization is the aim, then you
need to use -pbc nojump or inbox)
out of interest i performed the trjconv with .gro file as follows
trjconv -f abc.gro -s abc.tpr -pbc nojump -o output.gro
but when i viewed the output.gro in vmd i found most of my chains were
broken.
...which is due to a too large shift between the reference structure
(your final structure) and the first structure in your trajectory.
5.which file i have to give as input and what makes the difference (.xtc
file or .gro file?)
Either take the .tpr or take the .pdb file you started from (after
addition of hydrogens and such; the atoms must match).
then i tried wth .xtc file as input as follows
trjconv -f abc.xtc -s abc.tpr -pbc nojump -o output.gro
this time it was not found to be broken.
...which proves my point.
Waiting for any suggestions
Hope it helps,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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