[gmx-users] simulating two peptides in a box

[kartik mehra]

Dear GMX Users,

I am trying to set up a simulation box with two proteins. I have perused the
archives about the methodology of doing so. I tried the recommended option
of changing the number of protein molecules in the topology file to 2.
However when I run grompp after editconf and genbox, I get warning that the
number of co -ordinates do not match (since I had not updated the number of
solvent molecules ...) After updating the number of solvent molecules, when
I try running grompp again, it shows a warning that the 23644 atom names do
not match in top and gro files and that atom names from top files are being
chosen .

Upon subsequent mdrun, the system explodes after a 1-4 interaction warning.

I was wondering whether anyone could help me out on this ... I do understand
that the topic has been discussed pretty often but would appreciate any help
...


Cheers

Kartik

PS: I have not yet tried the other suggestion of translation and rotation
followed by concatenating the two files
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080707/9b64d249/attachment.html>