[gmx-users] soft-core

[Sai Kumar Ramadugu]

Hi
Well the tutorial in the following website has mentioned about the
importance of sc_alpha and sc-power. Also the manual gives you more
information.
http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial.

Regards
Sai

On Sun, Jun 13, 2010 at 6:56 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> fancy2012 wrote:
>
>> Dear GMX users,
>> when I generate the input file of MD simulation using grompp, I get this
>> error: ERROR: The soft-core power is 0 and can only be 1 or 2. I don't know
>> how to figure it out?  Could somebody give me a hand? Thanks very much in
>> advance!
>>
>
> You haven't specified a value for sc-power, so the default of zero is
> taken. Manual section 7.3.23.
>
> -Justin
>
>  Here is the mdp file:
>> cpp                 =  /lib/cpp
>> constraints         =  all-bonds
>> integrator          =  md
>> tinit               =  0.0
>> dt                  =  0.002   nsteps              =  25000     nstcomm
>>           =  1
>> nstxout             =  10000
>> nstvout             =  0
>> nstfout              =  0
>> nstlog              =  500
>> nstenergy           =  250
>> nstxtcout           =  1000
>> xtc_precision       =  1000
>> xtc_grps            =  Protein
>> nstlist             =  5
>> energygrps          =  Protein SOL
>> ns_type             =  grid
>> rlist               =  0.9
>> coulombtype         =  Reaction-Field
>> epsilon_r            =  78.0
>> rcoulomb            =  1.4
>> rvdw                =  1.4
>> Tcoupl              =  Berendsen
>> tc-grps             =  Protein SOL
>> ref_t               =  300 300
>> tau_t               =  0.1 0.1
>> Pcoupl              =  Berendsen
>> tau_p               =  1.0
>> compressibility     =  4.6e-5
>> ref_p        ;        =  1.0
>>
>> free_energy         =  yes
>> init_lambda         =  0.00
>> sc-alpha            =  1.51
>> All the best,
>> fancy
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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