Hi!
The answer is that I do not now critical it is.
I have seen some papers that seem to hint at it not being overly critical, but,
again, life does not come at a net charge.
You'd have to see for yourself in your system, given the observables that are
important I suppose.
Possibly we can implement this in the future, as there indeed seems to be some
interest in it, but that is not a task I can deal with currently.
/Per
10 mar 2011 kl. 10.52 skrev Yulian Gavrilov:
> Thanks again!
> Don't you know how to make a total charge = 0 in this case, if implicit salt
> concentration is not implemented currently? Or it is not critically?
>
> 2011/3/10 Per Larsson <per.lars...@sbc.su.se>
> Hi!
>
> Yes, except that in point 2, I'm not sure about the effects of explicit ions
> in an implicit solvent.
> Do deal with that properly one should use an implicit salt concentration, but
> that is not implemented currently.
> The choice of water-model with pdb2gmx is not important. You can choose
> 'None' here.
>
> Cheers
> /Per
>
> 10 mar 2011 kl. 10.39 skrev Yulian Gavrilov:
>
>> Thanks!
>> If I understand you correctly, I need to do this (?):
>> pdb2gmx
>> Adding ions (if I have no SOL, what is better to choose on this step?)
>> Minimization with mdp file, that includes these lines:
>> implicit_solvent = GBSA
>> gb_algorithm = {Still,HCT,OBC}
>> sa_algorithm=Ace-approximation
>> Equilibration (nvt, npt) and MD also with these lines in mdp files.
>>
>>
>> 2011/3/10 Per Larsson <per.lars...@sbc.su.se>
>> Hi!
>>
>> Starting an implicit solvent simulation works just as starting a "normal",
>> explicit solvent simulation, except there is no solvent molecules.
>> You should use version 4.5.3 for this though (4.0.5 will not work).
>>
>> Then you specify in the mdp-file implicit_solvent = GBSA and use pdb2gmx,
>> grompp, mdrun etc... as you otherwise would do.
>> The choice of the Born radii model is set by gb_algorithm = {Still,HCT,OBC}
>> and the non-polar solvation is calculated using
>> sa_algorithm=Ace-approximation.
>>
>> Cheers
>> /Per
>>
>> 10 mar 2011 kl. 10.10 skrev Yulian Gavrilov:
>>
>>> Dear, all
>>> I just begin to work in gromacs.
>>> I would like to run on a protein with amber99.
>>> Is there someone here that successfully did a protein simulation in
>>> GROMACS with implicit solvent and willing to explain the procedure and
>>> share the parameters used (especially force field).
>>>
>>> In mdout.mdp (gromacs 4.0.5) I found this lines. Can I add them to md.mdp?
>>> How to change this parameters correctly?
>>> What changes should be done on the previous steps? I mean, how to start a
>>> simulation with implicit solvent model from the very beginning?
>>> Sorry for primitive question, but I did not found any useful information
>>> about it for the begginers.
>>>
>>> ; IMPLICIT SOLVENT ALGORITHM
>>> implicit_solvent = No
>>>
>>> ; GENERALIZED BORN ELECTROSTATICS
>>> ; Algorithm for calculating Born radii
>>> gb_algorithm = Still
>>> ; Frequency of calculating the Born radii inside rlist
>>> nstgbradii = 1
>>> ; Cutoff for Born radii calculation; the contribution from atoms
>>> ; between rlist and rgbradii is updated every nstlist steps
>>> rgbradii = 2
>>> ; Dielectric coefficient of the implicit solvent
>>> gb_epsilon_solvent = 80
>>> ; Salt concentration in M for Generalized Born models
>>> gb_saltconc = 0
>>> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
>>> gb_obc_alpha = 1
>>> gb_obc_beta = 0.8
>>> gb_obc_gamma = 4.85
>>> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
>>> ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
>>> sa_surface_tension = 2.092
>>>
>>> --
>>> Sincerely,
>>> Yulian Gavrilov
>>>
>>> --
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>>
>>
>> --
>> gmx-users mailing list gmx-users@gromacs.org
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>>
>>
>>
>> --
>> Sincerely,
>> Yulian Gavrilov
>>
>
>
>
>
> --
> Sincerely,
> Yulian Gavrilov
>
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