[gmx-users] Protein-ligand interactions

Shrivastava, Indira indira at ccbb.pitt.edu
Thu Aug 18 15:34:01 CEST 2005

I am having a similar problem as Ulrich below, regarding ligand-protein interactions. I get different behaviour of the ligand when I run it on one node and two nodes.  So which one should I trust? the one-node simulation or two node-simulation? (the initial conditions are identical for both the simulations)

	-----Original Message----- 
	From: gmx-users-bounces at gromacs.org on behalf of Ulrich Omasits 
	Sent: Thu 8/18/2005 8:05 AM 
	To: gmx-users mailinglist 
	Subject: [gmx-users] stable trajectory?

	I'm simulating a protein-ligand system in a 20A-SPC waterbox using the
	gmx-ff and PME.
	My problem:
	The ligand should be high-affinity but in two out of five
	one-nanosecond-simulations the ligand detaches the protein!
	In one simulation the ligand seems to be stable (RMSD & RMSF look nice)
	but then the same simulation performed again (only starting velocities
	differ) delivers totally different results (ligand even detaches!).
	How can this happen!?! What can I do?
	Should I change the forcefield, the water-type, the box-type, the
	Could these changes affect the trajectory such drastically?
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