[gmx-users] Re: water dimer is gas phase
ndhumal at andrew.cmu.edu
Thu May 19 22:05:55 CEST 2011
if I set pbc=xyz in energy minimization mdp file then I get following error
ERROR: can only have neighborlist cut-off zero (=infinite)
with coulombtype = Cut-off or coulombtype = User and simple neighborsearch
without periodic boundary conditions (pbc = no) and
rcoulomb and rvdw set to zero
ERROR: One of the box lengths is smaller than twice the cut-off length.
Increase the box size or decrease rlist.
On Thu, May 19, 2011 3:57 pm, Vitaly Chaban wrote:
>> the equlibration file I used
>> title = cpeptid position restraining cpp
>> = /usr/bin/cpp
>> constraints = none integrator = md dt
>> = 0.001 ; ps !
>> nsteps = 1000000 ; total 1.0 ps. nstcomm =
>> nstxout = 10000 nstvout = 10000 nstfout
>> = 0
>> nstlog = 10 nstenergy = 10 nstlist =
>> ns_type = simple comm_mode = none coulombtype
>> = cut-off
>> vdwtype = cut-off rlist = 0.0 rcoulomb
>> = 0.0
>> rvdw = 0.0 pbc = no fourierspacing =
>> fourier_nx = 0 fourier_ny = 0 fourier_nz
>> = 0
>> pme_order = 4 ewald_rtol = 1e-5 optimize_fft =
>> yes ; Berendsen temperature coupling is on
>> Tcoupl = nose-hoover
>> tau_t = 0.1 tc-grps =system ref_t = 298 ; Pressure coupling is on
>> Pcoupl = NO ;Parrinello-Rahman
>> pcoupltype = isotropic tau_p = 2.0 compressibility
>> = 4.5e-5
>> ref_p = 1.0 ; Generate velocites is on at 300 K.
>> gen_vel = yes gen_temp = 298.0 gen_seed
>> = 173529
>> Is ther any thing wrong with my mdp files.
>> WHy they is so much change is cooridnates in the .pdb file.
> Set periodic conditions. This will restrict the coordinates to small
> Dr. Vitaly V. Chaban, Department of Chemistry
> University of Rochester, Rochester, New York 14627-0216
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