VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri Feb 24 2017 - 19:10:53 CST

Hey Sanim,

Going with what you said you don't say what error do you get?

Does the file load without errors and you dont see anything?

If you are combining 3 structures (with simple cat and assuming there are
no errors there with atom numbers) are they at the same point in space? If
the three structures are too far in space and you load everything you will
look at the centre which may not have anything I think.

To check for this when you load a gro file and assuming there is no error
the VMD main window should display the name of the file and the number of
atoms and frames. Do those fields get populated?

If yes then it's probably that the structures in the three files are
spatially too far apart. Try loading the three individual structures
seperately and see if they overlap.

If you are getting an error maybe mention that. Otherwise try seeing where
they are ... Otherwise write back and someone will help.

Best of luck.

/A

On Feb 25, 2017 13:09, "Sanim Rahman" <sanimr_at_mail.usf.edu> wrote:

Hello all,

I am having an issue viewing a .gro file I generated in GROMACS. I am aware
of issues highlighted in past threads about the structure not showing up at
all in VMD due to an " unexpected end-of-file reached" error. I fixed the
number of atoms within the system to remove this error and I am still
unsuccessful in viewing the structure. I also picked extreme dimensions for
my system by multiplying each dimension by 100 and that still failed.

The file was generated by combing three .gro files by using:

cat file1.gro file2.gro file3.gro > file4.gro

I have also tested the first three files and was able to view them
individually in VMD. So the error must have occurred in combining the
files. I will truly appreciate any assistance!

Regards,
Sanim Rahman