[gmx-users] multiple molecules in a box
turgaycakmak34 at gmail.com
Mon Jan 23 16:00:40 CET 2012
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
Could anybody help me please?
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