[gmx-users] Trouble using Encad in gmx-3.3

Erik Lindahl lindahl at sbc.su.se
Sat Oct 15 11:35:13 CEST 2005


> -------------------------------------------------------
> I used other Protein and the same happens, but in a different  
> residue. Both have in common being a Proline residue. I am not sure  
> if this is a bug or i am doing something wrong.

This was fixed in CVS a couple of days ago.
> By the way, As I have read from levitt's protocols, ENCAD is used  
> with ATOM based nb interactions, and they use their own cutoff  
> scheme, very similar to B.BrooKs's Force shifted spherical cutoff.  
> Is it posible to use that protocols? How can be selected in a mdp  
> file? I have not found info regarding that.

Actually, the original Encad setup is even more complicated, since it  
uses a group-based 1,4 interaction scaling.

Michael (Levitt, encad author) and I have worked together to  
parameterize and check things, and we're both perfectly happy with  
the charge group setup currently used in the Gromacs Encad version.

Although the Encad program by default uses shifted interactions with  
a cutoff at 6A and rlist to 8A, the encad *force field* was not  
explicitly parameterized for that. We're currently testing how it  
performs with PME, but you can use "encadshift" for both coulombtype  
and vdwtype with the cutoff/rlist above if you want.



Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214

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