[gmx-users] gmx insert_molecules problem
wumeng at shanghaitech.edu.cn
Tue Apr 4 08:59:01 CEST 2017
I am running a membrane protein MD simulation with Gromacs 5.1.4. I want to add some substrate molecules(acetate) to my system, and I used this command:
"gmx insert_molecules -f ###.pdb(include the ptotein, POPC, etc.) -ci act.pdb -o ###.pdb -nmol 48 -box 6.7 6.7 8.1 -try 500 -rot xyz",
but then I found many acetate molecules are put out of the system in the out .pdb.
Is that normol or wouldl affect the later MD process? If so, how can I fix it.
Any suggestions would be greatly appreciated. Thank you in advance!
All the best,
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