[gmx-users] creat .gro; select force field

[Justin A. Lemkul]

gromacs wrote:
> Hi users:
>  
> I run pure water MD. I need to run different water models. How can i get 
> spce.gro, which means how can i get .gro of spce water?
>  
> How can i get .gro of TIP4P?
>  

The answer to both of these questions can be found here:

http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file

> If i select TIP4P water model, which force field should i select?  you 
> know, i need .top, and .top should include force field.
>  
> If i select SPCE water model, which force field should i select?
>  

Water models, in principle, are not force field-dependent.  In theory you should 
be able to use any of them.

> I can find a spc216.gro, which is default solvent. I can use genbox to 
> generate a box of solvent (spc water). how can we use other solvent, so 
> we need to have the .gro of the solvent.
>  

See the link above.

-Justin

> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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