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 <[email protected]> To: Discussion list for GROMACS users <[email protected]> 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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 [email protected]. > * 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 [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
