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

[chris.neale at utoronto.ca]

> 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.

Your subject line is totally unrelated to your post. It's rather  
frustrating. Please try to fix that in the future.

Also you could have searched for:
protein out of box

and found your answer immediately. Please search in the future before asking.

For your convenience, You can see here:  
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions


>
> 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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