[gmx-users] trajconv

ann rose annrose.johns at gmail.com
Mon Jul 2 15:03:01 CEST 2007

Hi all

I am new to Gromacs: I am simulating pure polymer (22 monomers and 16 linear
chains) in vaccum and i have a few questions regarding the trjconv command.

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?

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?
3.the holes that i have mentioned before are accpetable or not?
4.is it can be the problem with VMD visualisation?

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

5.which file i have to give as input and what makes the difference (.xtc
file or .gro file?)

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.

Waiting for any suggestions

Thanking in advance
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