Quoting Luisa Calvanese <[EMAIL PROTECTED]>: > > > > > I'm doing a dynamic of a peptide in a mixture TFE/H2O ( 30/70 %).I'm using > this file.mdp : cpp = /lib/cppdefine = -DFLEX_SPC -DPOSRESconstraints = > all-bondsintegrator = mdtinit = 0.0dt = 0.002 ; ps !nsteps = 500000 ; total > 1000 ps.nstcomm = 1nstxout = 1000nstvout = 1000nstfout = 0nstxtcout = > 50xtc_precision = 1000nstlog = 1000nstenergy = 1000nstlist = 5rlist = > 1.0coulombtype = Cut-offrcoulomb = 1.4rvdw = 1.4epsilon_r = 1.0; Temperature > coupling is on in two groupsTcoupl = Berendsentc-grps = systemtau_t = > 0.1ref_t = 300; Energy monitoringenergygrps = system; Pressure coupling is > not onPcoupl = Berendsentau_p = 0.5compressibility = 4.5e-5ref_p = 1.0; > Generate velocites is on at 300 K.gen_vel = nogen_temp = 300gen_seed = 173529 > I 'd know if this file is correct.Thank you
Correct in what regard? You've given us no sense of what you're trying to accomplish, what force field you're using, etc. Is the use of this .mdp file generating some sort of problem? If so, describe the error and perhaps someone will have an idea. Other than that, it's not our job to do your homework for you. Look up parameters in the literature for similar systems and for use with your force field (i.e., rvdw, rcoulomb, etc.) and base your decisions off of what you find. -Justin > > Windows Live Mobile Collegati a Messenger dal tuo cellulare! > _________________________________________________________________ > Racconta le tue emozioni sul blog! > http://home.services.spaces.live.com/ ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
