[gmx-users] Protein-ligand interactions

[Shrivastava, Indira]

Thank you, David.
 

	-----Original Message----- 
	From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel 
	Sent: Thu 8/18/2005 9:51 AM 
	To: Discussion list for GROMACS users 
	Cc: 
	Subject: Re: [gmx-users] Protein-ligand interactions
	
	

	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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