Firstly I prepared urea box using amber99sb-ildn ff ,then do pdb2gmx of protein using amber99sb-ildn force field ,then do editconf with -d=1.46, genbox with -cs =urea_box generated previously and then energy minimization and then equilibration, segmentation fault occured at end. Please help me in solving this problem. Here is my em.mdp and pr.mdp file- em.mdp ;^M ; User spoel (236)^M ; Wed Nov 3 17:12:44 1993^M ; Input file^M ;^M cpp = /usr/bin/cpp^M define = -DFLEX_SPC^M constraints = all-bonds integrator = steep ^M nsteps = 50000 ; Energy minimizing stuff^M emtol = 1000^M emstep = 0.01^M nstlist = 1^M nstcomm = 100^M ns_type = grid^M rlist = 0.8 ^M coulombtype = PME^M rcoulomb = 0.8^M rvdw = 0.8 pbc = xyz fourierspacing = 0.12^M fourier_nx = 0^M fourier_ny = 0^M fourier_nz = 0^M pme_order = 4^M ewald_rtol = 1e-5^M optimize_fft = yes^M Tcoupl = no^M Pcoupl = no^M gen_vel = no^M ~
PR_nvt.mdp ;^M ; User spoel (236)^M ; Wed Nov 3 17:12:44 1993^M ; Input file^M ;^M title = Yo^M cpp = /usr/bin/cpp^M define = -DPOSRES^M constraints = all-bonds^M constraintalgorithm = LINCS^M integrator = md^M dt = 0.002 ; ps !^M nsteps = 50000 ; total 10 ps.^M nstcomm = 1000^M nstxout = 1000^M nstvout = 1000^M nstfout = 0^M nstlog = 10^M nstenergy = 10^M nstlist = 10^M ns_type = grid^M rlist = 1.4 coulombtype = PME^M rcoulomb = 1.4 rvdw = 1.4 fourierspacing = 0.12^M fourier_nx = 0^M fourier_ny = 0^M fourier_nz = 0^M pme_order = 4^M ewald_rtol = 1e-5^M optimize_fft = yes^M ; Berendsen temperature coupling is on in two groups^M Tcoupl = V-rescale^M tc-grps = System ^M tau_t = 0.1 ^M ref_t = 300 ^M ; Energy monitoring^M energygrps = System^M ; Pressure coupling is off^M On Wed, Mar 22, 2017 at 4:11 PM, Mark Abraham <[email protected]> wrote: > Hi, > > All of the advice there still applies to trying to move from a successful > energy minimization to a dynamical simulation. Without knowing all the > details of how you prepared everything, that advice is all anybody can say. > > Mark > > > > > On Wed, Mar 22, 2017 at 11:08 AM ISHRAT JAHAN <[email protected]> > wrote: > > > > I have reduced the force and timestep as given at > http://www.gromacs.org/ > > Documentation/Terminology/Blowing_Up > > <http://www.gromacs.org/Documentation/Terminology/Blowing_Up> > > <http://www.gromacs.org/Documentation/Terminology/Blowing_Up> but still > > getting an error like- > > Double precision normally gives you higher accuracy. > > You might need to increase your constraint accuracy, or turn > > off constraints alltogether (set constraints = none in mdp file) > > > > writing lowest energy coordinates. > > > > Back Off! I just backed up prion_em.gro to ./#prion_em.gro.1# > > > > Steepest Descents converged to machine precision in 726 steps, > > but did not reach the requested Fmax < 1000. > > Potential Energy = -1.7322245e+05 > > Maximum force = 8.0706294e+03 on atom 2216 > > Norm of force = 1.4435008e+02 > > > > if i proceed for pr with this result segmentation fault occured again. > > > > > -- > 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 [email protected]. > -- 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 [email protected].
