[gmx-users] Errors in Minimization using grompp

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Wed Jun 13 13:55:37 CEST 2012

Thank you for your answer.

> On 13/06/2012 6:44 PM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>> I want to do a minimization of the hydrogens of my protein. Only the
>> hydrogens.
> Doesn't really matter - nothing will move more than a fraction of an
> Angstrom unless it's horribly wrong, in which case not moving the heavy
> atoms won't help you.
>>   And I want to do this with implicit solvent.
> Probably not worth the effort if you're just preparing for MD.

Our goal is not an MD simulation of the protein. We plan a
Poisson-Boltzmann electrostatics calculation. For that we need the heavy
atoms as they are in the crystal structure (even 1 Angstroem movement
would be too much) with good hydrogen atom position.
We need to minimize, simulate, minimize, simulate the hydrogen atoms.
Implicit solvent is ok for us. (For a later MD run of the complete
protein, we will use explicit solvent).

This is the .mdp file:

define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  steep
nsteps              =  30000
vdwtype             =  cutoff
coulombtype         =  cutoff
epsilon_rf = 0
pbc                 =  xyz
nstlist             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.2
rvdw                =  1.2
rvdw_switch     = 0.7
comm-mode           =  angular
comm-grps           =  System
nstcgsteep = 1000
emtol               =  5.0
emstep              =  0.01
implicit_solvent    =  GBSA
gb_algorithm        =   HCT
nstgbradii          =  1
rgbradii            =  1
gb_epsilon_solvent  =  80
gb_saltconc       =  0
sa_algorithm        =  Ace-approximation
sa_surface_tension  = -1

Additionally I have a question according to the vdwtype and coulombtype.
Why do I have to set the two parameters to cutoff?


>> All the time when I try it there are errors in my .mdp file. Can you
>> please give me an example how such a .mdp file should look like.
> Every tutorial you've done will have an example EM .mdp file. Searching
> Google for some implicit solvent examples will provide some leads.
> Ultimately you need to learn how to create and manage one, so hoping one
> will appear and using it blindly is not terribly productive.

> Mark
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