[gmx-users] Temperature in simulation
shima_arasteh2001 at yahoo.com
Wed Oct 3 15:57:22 CEST 2012
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.
----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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.
> gmx-users mailing list gmx-users at gromacs.org
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 |
gmx-users mailing list gmx-users at gromacs.org
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users