[gmx-users] Errors in Minimization using grompp

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

Hi Justin,
I managed it with your help that the minimization run worked. Now I
prepared a .mdp file for the md run.
Can you please tell me if the following .mdp file is correct?

define          = -DPOSRES
integrator          =  md
constraints         =  all-bonds
emtol = 8
niter = 15
nsteps              =  50000
nstlist             =  1
ns_type             =  simple
rlist               =  0
comm-mode           =  angular
comm-grps           =  System
coulombtype         =  cut-off
vdwtype             =  cut-off
rcoulomb            =  0
rvdw                =  0
pbc                 =  no
epsilon_rf          =  0
implicit_solvent    =  GBSA
gb_algorithm        =   HCT
nstgbradii          =  1
rgbradii            =  0
gb_epsilon_solvent  =  80
gb_saltconc       =  0
sa_algorithm        =  Ace-approximation
sa_surface_tension  = -1


Thank you,
Eva


>
> On 6/13/12 7:55 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Hi!
>> 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.
>
> With restraints on heavy atoms, your positions will not deviate very much
> at
> all.  A 1 Angstrom movement would be huge in this case; I would expect
> your
> deviations to be orders of magnitude less.
>
>> We need to minimize, simulate, minimize, simulate the hydrogen atoms.
>
> I don't follow the logic here.  You say you need to do an EM of the H
> atoms in
> order to do some PBSA calculation with no MD, but here you're doing two
> iterations of EM and MD.
>
>> 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:
>>
>
> There are several problems here, most of which I've already stated, but
> I'll
> recapitulate them again.
>
>>
>> define              =  -DPOSRES
>> constraints         =  all-bonds
>> integrator          =  steep
>> nsteps              =  30000
>> vdwtype             =  cutoff
>> coulombtype         =  cutoff
>
> As Mark said, these settings should be "cut-off" not "cutoff."
>
>> epsilon_rf = 0
>> pbc                 =  xyz
>
> For an implicit system, periodicity should be set to "no" and grompp will
> warn
> you about using angular COM removal (invoked below) if you leave it set as
> is.
>
>> nstlist             =  1
>> ns_type             =  grid
>> rlist               =  1
>> rcoulomb            =  1.2
>> rvdw                =  1.2
>
> Finite cutoffs with implicit solvent will lead to instability and poor
> energy
> conservation.  These three lines (rlist, rcoulomb, rvdw) should be set to
> zero,
> unless you're satisfied with artifacts.
>
>> rvdw_switch     = 0.7
>
> This setting has no effect when using cutoffs.
>
>> comm-mode           =  angular
>> comm-grps           =  System
>> nstcgsteep = 1000
>> emtol               =  5.0
>
> Unless you've compiled with double precision, it is unlikely you will
> achieve a
> minimal force this low.  The use of restraints is going to preclude most
> movement in the system, so don't be surprised if grompp does not (and
> cannot)
> achieve this tolerance.
>
>> emstep              =  0.01
>> implicit_solvent    =  GBSA
>> gb_algorithm        =   HCT
>> nstgbradii          =  1
>> rgbradii            =  1
>
> This should also be set to zero if the above neighbor searching parameters
> are zero.
>
>> 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?
>>
>
> Because settings like PME don't make sense for implicit solvent
> calculations.
> Plain cutoffs with finite values are almost never adequate for any
> purpose, however.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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