[gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1
David van der Spoel
spoel at xray.bmc.uu.se
Wed Nov 21 09:10:30 CET 2007
Li Qiang wrote:
> Dear Gromacs Users,
> I wonder if it is normal for a protein to move out of the box during MD
> runs. periodic boundary conditions are applied. system is neutralized.
> 0.9nm for the distance between box side and protein.
first,please use a relevant mail subject.
second the answer is yes. See http://wiki.gromacs.org.
> the md.mdp for your reference:
> title = trp-Cage
> cpp = /usr/bin/cpp
> constraints = none
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 2500000 ; total 5000 ps.
> nstcomm = 1
> nstxout = 500 ; collect data every 1 ps
> nstvout = 0
> nstfout = 0
> nstlist = 5
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> rvdw = 1.0
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = berendsen
> tau_t = 0.1
> tc_grps = system
> ref_t = 498
> ; Pressure coupling is on
> Pcoupl = berendsen
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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