Hi Shahab, The best temperature to use is 298K as this is the temperature in which the force filed was parameterised. But, and this is a big but, I speculate that any errors you might have during the simulation due to the use of 310K is minimal and less then other inaccuracies in the force field.
Best, Itamar -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut =========================================== | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@med.monash.edu.au ============================================ ----- Original Message ----- From: shahab shariati <shahab.shari...@gmail.com> Date: Tuesday, February 23, 2010 9:45 pm Subject: [gmx-users] temperature To: gmx-users@gromacs.org > Hi gromacs users > > I want to run simulation of protein-dna interaction. > > what is best for temperature in mdp file: 1) 300K (default) 2) 310k > (physiologic temperature) > > > Any help will highly appreciated! >
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