[gmx-users] multiple molecules in a box

[Turgay Cakmak]

Hi gromacs users,

I have two different molecules, lets say A and B. I want to put 5 A
molecules and 5 B molecules in the same box.
I carried out the following steps.
   1)  For both A and B, I used *genbox* with *-nmol* flag separetely
and obtained the A_multiple and the B_multiple structure files.
   2)  Using *cat* command, I concatanated two structure files (A_multiple,
B_multiple) to get system.gro.
   3)  Using the *pdb2gmx*, I got conf.gro and topol.top of system..

But, I am not sure if this is the correct way? Because, when I look the
conf.gro at VMD, I saw that some part of the A molecule and B molecule had
overlapped.

Could anybody help me please?

Turgay
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120123/658e279b/attachment.html>