[gmx-users] error in grompp run

[reisingere at rostlab.informatik.tu-muenchen.de]

> On 13/06/2012 5:59 PM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Hi,
>> I want to do a MD simulation in vacuum.
>
> So don't turn on implicit solvent.
Sorry,
my fault. I want to do it in implicit solvent.
>
>>   So first I wanted to prepare the
>> files for that with "grompp".
>> But there I got the error that
>> "With GBSA implicit solvent, rgbradii must be equal to rlist"
>>
>> But the 2 values are the same in my .mdp file. Can you please show me
>> where the failure is?
>>
>>
>> define          = -DPOSRES
>> integrator          =  md
>> emtol = 1000.0
>> emstep         = 0.01
>> nsteps              =  50000
>> nstlist             =  1
>> ns_type             =  simple
>> rgbradii            = 0
>> rlist               =  0
>> coulombtype         =  cutoff
>> vdwtype             =  cutoff
>
> These are misspelled.
>
> See manual 7.3.9 for how to simulate without cut-offs.
>
> Mark
>
>> rcoulomb            =  0
>> rvdw                =  0
>> pbc                 =  no
>> epsilon_rf          =  0
>>
>> implicit_solvent    = GBSA
>> gb_algorithm        = HCT
>> gb_epsilon_solvent  = 78.3
>>
>> nstxout             = 1
>> nstfout             = 1
>> nstvout             = 1
>> nstxtcout           = 1
>> nstlog              = 1
>>
>>
>>
>> Thank you,
>> Eva
>>
>
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