dear users, i try to simulate a system of DNA (17 bp) and a protein (420 aa).
before i start my MD runs, i solvated the system in a cubic box (-d = 0.9) and started a minimization of it using the em.mdp file which you can see at the bottom of this email. unfortunately the minimization breaks (see below). And if it does not break, it is very slow (20 iterations take about 3 weeks). Can you see from the information i give to you, why this happens? The output of this minimizations looks something like: Steepest Descents: Tolerance (Fmax) = 1.00000e+00 Number of steps = 400 Step= 0, Dmax= 5.0e-04 nm, Epot= 4.14463e+16 Fmax= inf, atom= 2005 Step= 1, Dmax= 5.0e-04 nm, Epot= nan Fmax= 0.00000e+00, atom= 0 Step= 2, Dmax= 2.5e-04 nm, Epot= nan Fmax= 0.00000e+00, atom= 0 Step= 3, Dmax= 1.3e-04 nm, Epot= nan Fmax= 0.00000e+00, atom= 0 Step= 4, Dmax= 6.3e-05 nm, Epot= nan Fmax= 0.00000e+00, atom= 0 ... Hence there is an infinitive force acting on atom 2005 in my system, right ? First I looked at the coresponding file to figure ot which residue this atom belongs to. I then looked at the system using chimera as a viewer and found that is residue occurs several times in my system, which worries me a little bit. But there is no such thing like two atoms lying very close to each other which would explain the Fmax= inf, atom= 2005 line in the minimization. Has anyone got an idea of what is going wrong here or do you need more information about my used files. It would be of great help for my further work, so thanks a lot in advance and have a nice weekend Greetings ==================== em.mdp: title = Minimization of blah.pdb cpp = /usr/bin/cpp define = -DFLEX_SPC integrator = steep nsteps = 400 nstenergy = 5 nstxtcout = 5 nstlist = 5 ns_type = simple rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 pbc = xyz fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes constraints = none emtol = 1.0 emstep = 0.005 ==================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
