Hi Justin, So, do you suggest that after minimization, I should generate the velocity at 300K instead ? i.,e for equilibration,should following the set-up?
gen-vel = yes >> gen-temp = 300 >> gen-seed = -1 ________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Tue, August 2, 2011 8:26:16 PM Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP Justin A. Lemkul wrote: > > > Sanku M wrote: >> Hi Justin, >> I first performed two minimization using steep and l-bfgs as the method on >>the solvated system for each lambda. Then I ran a 500ps NVT simulation on >>minimized system ( for each lambda) where essentially same .mdp file was used >>except the following change: >> gen-vel = yes >> gen-temp = 280 >> gen-seed = -1 >> >> So, essentially, I heated the minimized system up from 280 K with ref_t 300K >>using sd integrator. But, here also I found the average temperature goes to >>303 >>K( instead of 300 K) . > > Unless you did simulated annealing in between, you didn't heat the system, > you >suddenly jolted the temperature, which is probably not stable. Maybe the >integrator/Langevin thermostat does not react well to these conditions. >Equilibrate under the conditions you wish to collect data. Your data >collection >uses NPT, so running NVT at a different temperature and suddenly changing the >temperature and introducing pressure coupling is not an appropriate procedure. >If nothing else, your data will be unreliable, even if your temperature was >correct. > Sorry, misread the previous .mdp settings. You're still using NVT, but the point about the temperature is still valid here. -Justin -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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
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