yes, that's right. Sincerely, Shima
----- Original Message ----- From: Peter C. Lai <p...@uab.edu> To: Discussion list for GROMACS users <gmx-users@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 <p...@uab.edu> > To: Discussion list for GROMACS users <gmx-users@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 > > -- > > gmx-users mailing list gmx-users@gromacs.org > > 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 gmx-users-requ...@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 > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@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 p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists