Hi Gromacs Users I'm new to list, but hope to get a little help from someone experienced with setting up some replica exhange simulations in explicit solvent. It keeps exploding after app. 50 to 200 ps simulation time. It runs fine up to there, and then suddently one or a couple of atoms get unstable and move to much between timesteps.
Heres what I have done. Build the peptide in extended configuration in pymol. Ran a 200 ps simulation with implicit solvent model to compact the structure. Generated a solvent box. Equilibrated the system for 200 ps. Generated a range of MDP file with varying temperatures and made individual .tpr files Ran the simulation with the switches -multi 16 -replex 1000 I tried to troubleshoot a little with lowering the dt and equilibrating and minimizing more. Also tried different temperature coupling, as I'm not sure what is the most appropriate for REMD simulations. Is there something wrong with the parameters of the mdp file? title = Yo cpp = /lib/cpp include = -I../top define = integrator = md dt = 0.002 nsteps = 10000000 nstxout = 10000 nstvout = 10000 nstlog = 10000 nstenergy = 1000 nstxtcout = 1000 xtc_grps = Protein energygrps = Protein SOL nstlist = 10 ns_type = grid rlist = 0.8 coulombtype = PME rcoulomb = 0.8 rvdw = 0.8 tcoupl = Berendsen tc-grps = Protein SOL tau_t = 0.1 0.1 ref_t = 300 300 Pcoupl = Berendsen tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = all-bonds Best Regards Esben
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