[gmx-users] Temperature in simulation

[Shima Arasteh]

yes, that's right.

 
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 5:37 PM
Subject: Re: [gmx-users] Temperature in simulation

It sounds like you want to report that you created a bilayer, equilibrated it
at 310K then inserted the protein and ran MD of the embedded system at 300K?

On 2012-10-03 06:57:22AM -0700, Shima Arasteh wrote:
> 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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> ==================================================================
> Peter C. Lai            | University of Alabama-Birmingham
> Programmer/Analyst        | KAUL 752A
> Genetics, Div. of Research    | 705 South 20th Street
> pcl at uab.edu            | Birmingham AL 35294-4461
> (205) 690-0808            |
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-- 
==================================================================
Peter C. Lai            | University of Alabama-Birmingham
Programmer/Analyst        | KAUL 752A
Genetics, Div. of Research    | 705 South 20th Street
pcl at uab.edu            | Birmingham AL 35294-4461
(205) 690-0808            |
==================================================================

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