[gmx-users] g_sas query

[Mark Abraham]

On 7/05/2011 4:36 PM, Anirban Ghosh wrote:
> Hello Tsjerk,
>
> Thanks for the reply.
> But if I consider the ions also in the calculation group, then it is 
> not wrong. Right?

Only you know where your ions are, and whether their contribution to 
surface area means anything. Make the hybrid groups accordingly.

Mark

> Thanks,
>
> Anirban
>
> On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar <tsjerkw at gmail.com 
> <mailto:tsjerkw at gmail.com>> wrote:
>
>     Hey Anirban,
>
>     I would consider the ions part of the solvent. But the procedure
>     is right.
>
>     Cheers,
>
>     Tsjerk
>
>>     On May 7, 2011 7:35 AM, "Anirban Ghosh"
>>     <reach.anirban.ghosh at gmail.com
>>     <mailto:reach.anirban.ghosh at gmail.com>> wrote:
>>
>>     Hi ALL,
>>
>>     I want to calculate the SASA of a protein embedded in a bilayer
>>     along with water and ions. So while using g_sas I understand that
>>     I need to supply all non-solvent atoms as calculation group and
>>     Protein as the output group. So I need to make a group with
>>     Protein+Lipid+Ions as the calculation group. Right?
>>     Thanks a lot in advance.
>>
>>     Regards,
>>
>>     Anirban
>>
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