[gmx-users] Temperature in simulation

[Shima Arasteh]

I see that the velocities will be reassigned, but what I'm concerned about, is reporting the results in a paper. How would it be?

Thanks for your suggestion Peter.

 
Sincerely,
Shima


----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Wednesday, October 3, 2012 5:16 PM
Subject: Re: [gmx-users] Temperature in simulation

You should do NVT equilibration to your target temperature. Your system is
already heavily changed between the equilibrated full bilayer and the 
embedded protein system so velocities will be reassigned anyway.

On 2012-10-03 06:39:39AM -0700, Shima Arasteh wrote:
> 
> 
> Hi all,
> 
> I want to insert a protein in POPC lipid bilayer. 
> 
> First of all, I simulated POPC in water in 310 K. Now, I want to insert protein in lipid-water. To simulate protein-lipid-water system I want to run NVT in 300 K and then go on. Does anybody know it would be  incorrect logically ? 
> 
> 
> As I know, 10 degree increase in temperature of system, may result in some troubles in my small protein. But I guess this would not happen for lipid bilayer.
> 
> 
> Thanks in advance for your suggestions.
> 
> 
> Sincerely,
> Shima 
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