Dear Gromacs users
I'm having a bit of a trouble with genbox: I want to insert 4 PLM (palmitate) molecules at random positions in my simulation. So I tried running: genbox -cp cent_tim.gro -ci plm.gro -nmol 4 -o 4PLM_tim.gro -seed 100 pdb2gmx -f 4PLM_tim.gro -o 4PLM_tim.gro -p -ter I got a GRO file and indeed there were 4 PLM molecules. When I ran the same script again, I got the exact same GRO file. Meaning, the positioning of the PLM molecules wasn't truly random. After reading the Description on http://www.gromacs.org/documentation/reference/online/genbox.html I saw that the -ci flag supposedly works only if I insert one molecule. So I tried a different approach - to add a single PLM four times like so: # Palmitate No.1 genbox -cp cent_tim.gro -ci plm.gro -nmol 4 -o 1PLM_tim.gro pdb2gmx -f 1PLM_tim.gro -o 1PLM_tim.gro -p -ter # Palmitate No.2 genbox -cp 1PLM_tim.gro -ci plm.gro -nmol 1 -o 2PLM_tim.gro pdb2gmx -f 2PLM_tim.gro -o 2PLM_tim.gro -p -ter # Palmitate No.3 genbox -cp 2PLM_tim.gro -ci plm.gro -nmol 1 -o 3PLM_tim.gro pdb2gmx -f 3PLM_tim.gro -o 3PLM_tim.gro -p -ter # Palmitate No.4 genbox -cp 3PLM_tim.gro -ci plm.gro -nmol 1 -o 4PLM_tim.gro pdb2gmx -f 4PLM_tim.gro -o 4PLM_tim.gro -p -ter I got a different GRO than the one I got when adding the whole 4 of PLM in one line, but still, If I run the same batch of commands again, I get the same GRO file. If I run the first batch 50 times, each time I'll get the same GRO file as before. Same is true for the second batch. Meaning the positioning is not random. I tried fiddling with it some more (removing "-seed 100" etc., ) and still the result is the same. Thank you very much in advance and best regards, Shay Amram
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