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
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