Hi Mark,
David was installing a new server - as soon as I get an IP for it
I'll enter it in the gromacs DNS and we can put a wiki online :-)
David - any update?
Cheers,
Erik
On May 16, 2007, at 10:51 AM, Mark Abraham wrote:
Mark Abraham wrote:
Roughly speaking, a gromacs .top file has the same sort of
information as a .psf file, but VMD won't read one natively.
Instead, give VMD a structure file (.gro, .g96, .pdb or anything
else) that corresponds (in the same order) to the atoms that are
saved in your trajectory in place of the .psf file, and then load
the trajectory (.trr or .xtc) into that molecule in the same way
you would a .dcd file (see the VMD manual if you don't understand
this step). VMD will guess the atom connectivity based on the
original structure you give it - you should not expect this
connectivity to correspond perfectly to that in your .top file.
The gromacs tool ngmx can do a rough and ready visualization, if
the right X libraries exist and ngmx was installed. See "man ngmx"
for info.
Mark
This is classic Wiki material... how are we going with this?
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.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
_______________________________________________
gmx-users mailing list [email protected]
http://www.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
