[gmx-users] Protein-ligand interactions

[David van der Spoel]

On Thu, 2005-08-18 at 09:34 -0400, Shrivastava, Indira wrote:
> Hi,
> 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)
Both.

You need more and/or longer simulations.
And verify the start structure.

> Indira 
> 
> 	-----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 
> 	Cc: 
> 	Subject: [gmx-users] stable trajectory?
> 	
> 	
> 
> 	Hi,
> 	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
> 	PME-parameters,...?
> 	Could these changes affect the trajectory such drastically?
> 	
> 	Thanks
> 	Ulrich
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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