Dear gmx-users, We currently performed simulations to study the effect of repulsive electrostatic interactions on the stability of a silk-like protein. The amino acid sequence of our protein is the following: Lys [ (Gly-Ala)_3 Gly (Gln or Lys)]_3 where (Gln or Lys) means that we alternatively have Lys or Gln in that position starting with Gln. We start our simulations with three of these proteins on top of each other (each having a beta-sheet structure).
We performed two set of Replica exchange simulations with implicit solvent (see below for an mdp file). In one the lysine residues are positively charged and in the other they are neutral (LYN). Surprisingly, we see that the charged protein is more stable than the neutral one, i.e., repulsive electrostatic interactions are helping the charged protein not to unfold!!! I suppose this is not a normal behavior. What could go wrong in such simulations that results in this? Thanks for your time, Regards, Saber mdp file for one of the replicas: ; RUN CONTROL PARAMETERS integrator = sd tinit = 0 ; Starting time dt = 0.002 ; 2 femtosecond time step for integration nsteps = 10000000 ; OUTPUT CONTROL OPTIONS nstxout = 50000 ; Writing full precision coordinates every nanosecond nstvout = 50000 ; Writing velocities every nanosecond nstfout = 0 ; Not writing forces nstlog = 500 ; Writing to the log file every step nstenergy = 500 ; Writing out energy information every step nstxtcout = 500 ; Writing coordinates every 5 ps energygrps = System ; NEIGHBORSEARCHING PARAMETERS nstlist = 0 ns-type = simple pbc = no rlist = 0 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = cut-off rvdw = 0 rcoulomb = 0 ; Temperature coupling tc-grps = System ld_seed = -1 tau_t = 0.1 ref_t = 298.00, ; implicit solvent implicit_solvent = GBSA gb_algorithm = OBC rgbradii = 0 gb_epsilon_solvent = 80 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 300 comm_mode = Angular ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 -- 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
