[gmx-users] question regarding high temperature simulation in Gromacs

Dr. Puspita Halder puspita at cse.iitkgp.ac.in
Fri Jul 6 09:42:46 CEST 2018

Hi All,

Thanks for your helpful suggestions. I'd like to share the method that I am following now for simulating my protein at high temperature. First, I carried out energy minimization run for my protein system using steepest decent method. Then I performed nvt equilibration run for 100-200 ps at 300K followed by npt equilibration at the same temperature and at 1atm pressure for 1-2 ns with protein position restrain. Then I used simulated annealing protocol (without position restrain and under nvt condition) for reaching the temperature of the system to 500K starting from the structure of 300 K npt simulation with 50K temperature increment each time followed by 2-4 ns of equilibration run at respective temperature. Finally I did the production run at 500 K for 30-40 ns under nvt condition. Do you think that the protocol I am using is ok ? The problem is I am getting high value of pressure average (~3000-4000) for the simulated annealing run. Please share your comments or suggestion regarding this.

Thanks for your help.

Puspita Halder

----- Original Message -----
From: "Dr. Puspita Halder" <puspita at cse.iitkgp.ac.in>
To: "gromacs org gmx-users" <gromacs.org_gmx-users at maillist.sys.kth.se>
Sent: Wednesday, July 4, 2018 12:41:56 PM
Subject: question regarding high temperature simulation in Gromacs

Hi All,

I have been recently using Gromacs 5.1.4 version for simulating my protein systems (mainly prion protein and some of its mutants). I'd like to perform high temperature (400K or 500K) simulations with those. Now my question is what should be the values of the simulation parameters e.g., compressibility, tau_p or tau_t at 400K or 500K? I used compressibility = 4.5e-5 and tau_p = 2.0 and tau_t = 0.1 for pressure and temperature coupling for simulations at 300K. What other parameters should I change for high temperature simulations? Should I always use simulated annealing protocol for simulations at higher temperature or I can directly heat the system to such higher temperatures? Any comments or suggestions in this regard will be highly appreciated.

Thanks for your help in advance.

Puspita Halder

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