For more details, my system also has another cofactor with similar characteristics (FAD), I mean with hydroxyl groups but all is going fine with it so far (equilibration step).
As I wrote before I did the following steps: 1- vaccuum minimization 2- solvating 3- neutralizing 4- minimization 5- heating (increases by temperature ramp and using position restraints for all the components of the system) 6- equilibration (3 sequencial steps: the first step (NVT with a v-rescale thermostat) is where the system crashes) here the .mdp file of this first equilibration step: define = integrator = md dt = 0.001 ; ps ! nsteps = 150000 ; 150 ps nstcomm = 1 nstxtcout = 10000 xtc-precision = 10000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 10000 nstenergy = 10000 ; Non-bonded Interactions nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 vdwtype = cut-off rvdw = 0.9 vdw-modifier = Potential-shift-Verlet ; Berendsen temperature coupling is on in two groups Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ref_t = 310 ; Energy monitoring energygrps = System DispCorr = EnerPres ; Isotropic pressure coupling is now off Pcoupl = no Pcoupltype = isotropic tau_p = 5.0 compressibility = 4.6e-5 ref_p = 1.0 ; Generate velocites is off at 310 K gen_vel = no gen_temp = 310 gen_seed = -1 ; Constraints constraint_algorithm = lincs lincs_order = 8 constraints = all-bonds lincs-warnangle = 60 disre = simple Thank you in advance Best regards Juan José 2017-05-16 13:03 GMT+02:00 Juan José Galano Frutos <juanj...@gmail.com>: > Hi there: > > I am simulating a protein which include as a cofactor a molecule bearing > some hydroxyl groups. The system is crashing from the begining of the > equilibration step (after the following steps: vaccuum minimization, > solvating, neutralizing, minimization, heating) due to -in all the > replicas- to hydroxyl bonds that steadily rotated more than 60 and even 90 > degrees. > I checked the structures and the systems looking for either water or > protein parts in so close contact with this hydroxyl groups, but it was not > the case. Then I proceeded to re-minimize again the systems after the > heating step and afterward to relaunch the equilibration step, but again > the same happened. I also checked the topology file of this cofactor but > all seems to be fine, I mean charges. > Then, what could be happening? Is it common this behaviour in hydroxyl > groups?Any help please.... > > Thanks > > Best > > Juan José Galano Frutos > > Department of Biochemistry and > Molecular and Cellular Biology, > Faculty of Sciences, > University of Zaragoza > Pedro Cerbuna # 12, 50009 > Zaragoza (Spain) > +34 976 76 28 06 <+34%20976%2076%2028%2006> > > Institute for Biocomputation and > Physics of Complex Systems (BIFI) > Mariano Esquillor, Edificio I + D - 50018 > Zaragoza (Spain) > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
