[gmx-users] what are the options for implicit solvent in Gromacs?

[Jagannath Mondal]

Hi David,
            Thanks for your email. But then  what is the purpose of   
option like  gb_algorithm, nstgbradii =1 etc.
     Is there any way I can do implicit solvent simulation using any  
other interface?
Thanks,

  Jagannath

On Apr 12, 2007, at 5:06 PM, David van der Spoel wrote:

> Jagannath Mondal wrote:
>> Hi,
>>      I am trying to learn how to use implicit solvent model for  
>> PMF calculation. For that ,I wanted to know what are the options  
>> for implicit solvent present in gromacs. But I could not find any  
>> documentation regarding that. I searched  mailing list and found  
>> that there has been some query on the documentation but I could  
>> not find any suitable reply. In one of the reply, David suggested  
>> using following command:
>>     touch grompp
>>         grompp
>>    But it does not show all the available option for implicit  
>> solvent model  gromacs has got. it shows   implicit solvent= no.
>>     There were some older mail (before 2006) where it  was said  
>> that gromacs has not gor implicit solvent model. But I hope that  
>> latest version has got implicit solvent model. Can anyone suggest  
>> any documentation where I can find the availble options for  
>> implicit solvent model as well as the other options for  
>> Generalized Born model?
>>    Thanks in advance,,
>>      Yours sincerely,
>
> sorry. no implicit solvent.
>
>>
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>
>
> -- 
> David.
> ______________________________________________________________________ 
> __
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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