[gmx-users] Is it flexible water or all the bond, angle fixed? what is the potential energy in Gromacs 4.5 using OPLSAA

[Justin A. Lemkul]

MD wrote:
> Hi gromacs experts,
>  
> I used gromacs 4.5.3. my system has only spce water, no other types.
>  
> In .mdp file,
>  
> I used the following parameters;
>  
> define =
>  
> constraints = none
> constraint-algorithm = Lincs
>  
> Can u tell me  Is it flexible water or all the bond, angle fixed using 
> the above setting?
>  

Look at spce.itp and/or your md.log file.  If the #ifdef FLEXIBLE statement is 
not invoked, the SETTLE algorithm is used.

>  
> what is the equations of potential energy in Gromacs 4.5 using OPLSAA?
>  

The components of various functional forms are described in the manual.

-Justin

>  
> Best regards
> 
> 
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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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