[gmx-users] settingparameters for energy minimization

[Justin A. Lemkul]

vivek sharma wrote:
> Hi justin,
> Thank you very much for your quick reply. I also want to know is there 
> any other option than PRODRG to generate topology files for the 
> non-standard residues ?

The Gromacs tool x2top can generate topologies, but I don't believe it is very 
advanced yet.  There is also some user-contributed code called "topolbuild," but 
I have not used it.

> As PRODRG server usually go down these days.
> 

It's running fine right now, and I've never had a problem with it.  Does it go 
down frequently?

-Justin

> With thanks,
> Vivek
> 
> 2009/3/2 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     vivek sharma wrote:
> 
>         Hi There,
>         I am trying to do energy minimization of some protein molecule,
>         and I have following queries for the same.
>         1. Can I define some RMSD tolerance, such that RMSD value of the
>         molecule during the energy minimization will not vary more than
>         some predefined value.
> 
> 
>     No, nor would it do much good.  Do you expect the RMSD to change
>     much during EM?  I usually see an RMSD no greater than 0.2 Ang.
> 
> 
>         2. Which integrator is better to use SD or CG ?
> 
> 
>     That depends on your definition of "better."  Try both and see which
>     results you think are more reliable, otherwise consult some textbook
>     material or literature references on the algorithms.
> 
> 
>         3. what algorithm should be used for  long-range electrostatic
>         interaction PME or cut-off.
>          
> 
> 
>     PME is more accurate than cut-off.
> 
>     -Justin
> 
>         Please suggest for the above queries.
> 
>         With thanks,
>         Vivek
> 
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================