[gmx-users] OPLS-AA time step

Thomas Stockner stockner at ucalgary.ca
Thu May 20 19:14:11 CEST 2004

> On Thu, 2004-05-13 at 20:16, gerph at correo.unam.mx <http://www.gromacs.org/mailman/listinfo/gmx-users> wrote:
>>/ Dear gromacs user, 
/>>/ Until now I have simulations of my protein using default atoms definition for
/>>/ aromatics residues,  
/>>/ but when I tried to use "-dummy aromatics" option I have a consistent error (I
/>>/ tried whit differents proteins) 
/>>/ for the first residue, 
/>>/ WARNING: atom H is missing in residue SER 1 in the pdb file 
/>>/          You might need to add atom H to the hydrogen database of residue SER 
/>>/          in the file ff???.hdb (see the manual) 
/>>/ There were 1 missing atoms in molecule Protein_B 
/>>/ Number of bonds was 7439, now 7439 
/>>/ Opening library file /usr/share/gromacs/top/ffgmx2.ddb 
/>>/ Fatal error: Invalid directive NH3 in dummy database ffgmx2.ddb 
/>>/ I tried with -ter -missing  to modify the NH3 if this corresponding to the
/>>/ termini residue and  
/>>/ include only one H missing, but it does not work. Before try modified the ddb
/>>/ file I want to know if  
/>>/ there some alternative to fix this problem. I use gromacs 3.2.1. .
> With -dummy aromatics you should use the gromos96 force field.
> With -dummy h you can also use the OPLS force field (if you need all
> atoms). ffgmx2 is deprecated.

Dear gromacs users, 

can I increase the maximal allowed time step form 2 to 5 fs, when using 
OPLS-AA with -dummy hydrogens?



Thomas Stockner
Department of Biological Sciences
Biol. 414-416
2500 University Drive NW
Calgary, AB T2N 1N4
Phone: (403) 220-2439
Fax: (403) 289-9311
email: stockner at ucalgary.ca

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