namd simulation​:protein,l​igand,lipi​d,water and ions

From: Marlet Martinez (
Date: Tue Aug 28 2012 - 12:30:04 CDT

Dear NAMD users,

Recently I ran a simulation that consits of protein, ligand, lipid, water
and ions. It was quite complicated to run it, I had to run several
different simulations,inactivated "tcl forces"in the second configuration
file and I could run my simulation, however now that I am analyzing my
trayectory (last restart coord file) I found that something wrong happened
because lipid membrane and protein were compacted and waters are all
separated from the protein,

Do you have any suggestion?

Thanks in advance,


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