You are right and I will insert the native protein in membrane. To do so, I want to set the temperature of nvt.mdp file to 300 K, however I want to use the result output of memrane simulated in 310 K for 50 ns. Through your earlier suggestions, I got that velocities would be reassigned in new simulation and 10 degree is not a thing to be concerned in my system. Here, I'd like to know if I am criticized for using this difference between temperatures? Thanks for all your suggestions, that are all kind of you :-)
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <[email protected]> To: Discussion list for GROMACS users <[email protected]> Cc: Sent: Wednesday, October 3, 2012 8:44 PM Subject: Re: [gmx-users] Temperature in simulation On 10/3/12 10:16 AM, Shima Arasteh wrote: > Actually, I want to study this system of protein-membrane, trying to > replicate in vitro conditions and then studying function of the protein. > > I simulated the protein in water to see the usual result : losing its native > configuration. Then, I am trying to insert the protein in membrane to study > its function. > > Inserting an unfolded (or partially unfolded) protein into a membrane and hoping it reflects reality may or may not be wise. If you want to compare water vs. membrane environments, those should be two separate simulations, both starting from the same (presumably) native state of the protein. If you're hoping that the protein will re-fold within the membrane, you're probably making a large number of assumptions, most of which may not hold up under scrutiny. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
