[gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1

[David van der Spoel]

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.

> thanks
> 
> 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