[gmx-users] IMPLICIT SOLVENT IN AMBER

[Per Larsson]

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.larsson at 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.larsson at 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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>> 
>> 
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>> 
>> -- 
>> Sincerely,
>> Yulian Gavrilov
>> 
> 
> 
> 
> 
> -- 
> Sincerely,
> Yulian Gavrilov
> 

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