[gmx-users] IMPLICIT SOLVENT IN AMBER

[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 (?):
>
>    1.
>
>    pdb2gmx
>    2.
>
>    Adding ions (if I have no SOL, what is better to choose on this step?)
>    3.
>
>    Minimization with mdp file, that includes these lines:
>
>    implicit_solvent = GBSA
>
>    gb_algorithm = {Still,HCT,OBC}
>
>    sa_algorithm=Ace-approximation
>    4.
>
>    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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