[gmx-users] query about protein-ligand complex

sangeeta sangeeta at bic.boseinst.ernet.in
Fri Jun 30 14:22:44 CEST 2006

Dear all,

I am trying to run the dynamics of protein-ligand complex following the 
tutorial "GROMACS Tutorial for Drug_Enzyme Complex version 3.3.1"
. I am running position restricted dynamics of the 91az8.pdb protein as 
mentioned in the tutorial trp.pdb & drg.pdb)in a Linux server machine, I can 
not understand why it is taking such a long time, the machine is not busy 
with any other jobs.I ran it before & I stopped  the run at 1200 min, now it 
is going for about 215 min, &  step6.pdb, step7.pdb etc files are being 
formed, I can not undersyand whether I am doing any wrong step, why it is 
taking such a long time , I don't know , please help.

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