[gmx-users] Re: water dimer is gas phase

[Nilesh Dhumal]

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.


Nilesh

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             =
>>  1
>> nstxout             =  10000 nstvout             =  10000 nstfout        
>>     =  0
>> nstlog              =  10 nstenergy           =  10 nstlist             =
>>  10
>> ns_type             =  simple comm_mode           = none coulombtype      
>>   = cut-off
>> vdwtype             = cut-off rlist               =  0.0 rcoulomb        
>>    =  0.0
>> rvdw                =  0.0 pbc                 =  no 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
>> 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.
>>
>>
>
>
>
> Nilesh:
>
>
> Set periodic conditions. This will restrict the coordinates to small
> numbers.
>
>
> --
> Dr. Vitaly V. Chaban, Department of Chemistry
> University of Rochester, Rochester, New York 14627-0216
> --
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