Is simulated annealing carried out during NPT or in the production run? Akash
-----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: 20 September 2017 03:20 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Running MD simulations at a particular temperature On 9/19/17 4:25 PM, Pandya, Akash wrote: > Hi all, > > I want to run my MD simulation at 65 degrees Celsius. The mdp file has a > field as shown below: > > ref_t = 338.15 338.15 ; reference > temperature, one for each group, in K > > I am wondering whether the simulation has already reached the desired > temperature or does it heat up to 65 degrees throughout the course of the > simulation? I hope this makes sense. The answer depends on what you're doing. If you've set "gen-vel = yes" and "gen-temp = 338.15" then you are initializing a simulation with random velocities according to a Maxwell distribution at that temperature. If your system is at some other temperature and you're just trying to use a thermostat to force a change in that temperature, there's no real "warming" going on, rather the thermostat is going to push the velocity distribution towards the desired temperature. Warming a system is done via simulated annealing options. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
