[gmx-users] RE:

[Mungikar, Amol Arvind (UMR-Student)]

Thank you very much Ilya, this definitely helps, I got the direction now, I will work on it now ....
thanks 
amol

	-----Original Message----- 
	From: gmx-users-admin at gromacs.org on behalf of Ilya Chorny 
	Sent: Sun 3/14/2004 10:52 AM 
	To: gmx-users at gromacs.org 
	Cc: 
	Subject: [gmx-users] RE:
	
	

	This has been done many times before in the literature. The simplest naive 
	way to do is just to run 
	an equillibrium simulation and calcualte P(phi,psi). If you want to get to 
	phi psi angles which are 
	not accessable on the time scale of your simulation then you will have to 
	use a restraining potential inored to 
	explore a region of torsional space. This is called umbrella sampling and I 
	believe gromacs has implimented 
	some umbrella sampling but I'm note sure if they allow for  torsional 
	resraints? 

	Ilya 

	-----Original Message----- 
	From: Mungikar, Amol Arvind (UMR-Student) 
	[mailto:gmx-users-admin at gromacs.org]On Behalf Of Mungikar, Amol Arvind 
	(UMR-Student) 
	Sent: Saturday, March 13, 2004 5:18 PM 
	To: gmx-users at gromacs.org 
	Subject: 


	Dear all, 
	I was wondering if anybody has used gromacs for calculation of free energy 
	surface of the protein as a function of phi and psi (torsional angles). If 
	yes kindly let me know if this is possible, or I have to make some changes 
	to the source code. 
	Thank you very much in advance! 
	Amol 

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