swapnil chavan wrote:
Hi all,
I am running coarse grain MD simulations first time and unable to see
bonds after loading .gro and .trr file in vmd.
I have made initial .pdb by atom2cg.awk, then .itp by seq2itp.pl
<http://seq2itp.pl>. With use of this, I prepared .pdb ,.itp and .top
and subjected to mdrun. During analysis in vmd I can't see any bond
among this grains. I have used coarse_grained.tcl to make it possible
but I got error of
- couldn't execute "/usr/export/gromacs-3.3.3/bin/gmxdump": no such file
or directory.
After copying the gmxdump to /usr/export/gromacs-3.3.3/bin I got another
problem i.e.
It's probably better to change the path in the .tcl script, rather than move
around executables within the root filesystem, but that's just my opinion.
g_cg -tpr min.tpr
[ g_cg ] Processing "min.tpr"...
can't read "N": no such variable
What is g_cg? It's not official Gromacs, but hopefully it comes with some sort
of documentation as to how to use it.
Can anyone please let me know whether I am correctly doing this coarse
grain md. Please guide me to analyse my trajectory of coarse grain md in
which I can't see anything except beads. Your help will be deeply regarded.
Thank you in advance.
Have you tried top2psf.pl? Not that coarse_grain.tcl won't work, but it's
another option. It's available here:
http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD
-Justin
Sincerely,
Neel
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
