OK, so if i got this right all I have to do is add another line in the mdp file with refcoord_scaling = com? I thought that i had to make a substitution in one of the existing terms.
Thanks. ________________________________ De: Justin Lemkul <[email protected]> Para: Eduardo Oliveira <[email protected]>; Discussion list for GROMACS users <[email protected]> Enviadas: Segunda-feira, 17 de Dezembro de 2012 11:57 Assunto: Re: [gmx-users] mdp file warnings On 12/17/12 8:55 AM, Eduardo Oliveira wrote: > Hi, > > I'm setting my system but when I run grompp I get a warning and the program > terminates. It says the following: > > You are using pressure coupling with absolute position restraints, this will > give artifacts. Use refcoord_scaling option. > > > I want to try it but i don't know where to change this term in the mdp file. > Any help? > Location within the file is irrelevant. For most cases, you want "refcoord_scaling = com." See the numerous discussions on this topic in the list archive. -Justin > title = 500ps_pr_fixo > cpp = /lib/cpp > define = -DPOSRES > integrator = md > tinit = 0 > dt = 0.002 > nsteps = 250000 ; total 500 ps > comm-mode = Linear > nstcomm = 1 > nstxout = 500 > nstvout = 20000 > nstfout = 20000 > nstlog = 1000 > nstenergy = 100 > nstxtcout = 500 > xtc-precision = 1000 > energygrps = Protein SOL NA > nstlist = 5 > ns_type = grid > pbc = xyz > rlist = 1.0 > domain-decomposition = no > coulombtype = PME > rcoulomb = 1.0 > epsilon-r = 1 > vdw-type = Cut-off > rvdw = 1.4 > DispCorr = EnerPres > optimize_fft = yes > Tcoupl = V-rescale ;berendsen > tc-grps = Protein Non-protein > tau-t = .1 .1 > ref-t = 310 310 > gen_vel = yes > gen_temp = 310 > gen_seed = 173529 > Pcoupl = berendsen > Pcoupltype = Isotropic > tau-p = 1 > compressibility = 4.5e-5 > ref-p = 1 > constraints = all-bonds > constraint-algorithm = Lincs > unconstrained-start = no > Shake-SOR = no > shake-tol = 1e-04 > lincs-order = 4 > lincs-warnangle = 30 > morse = no > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
