[gmx-users] grompp error with gromacs-3.3

[Erik Lindahl]

Hi,


On Oct 16, 2005, at 6:34 PM, Lei Zhou wrote:

> Hi,
> thanks for the reply. I have removed those two 0's from the "imp"  
> part and now the grompp (of 3.3) is working. The modified  
> ligand.itp is looks like this:
> 3 1 4 13 2 35.3 334.8 35.3 334.8 ; imp C2* O2* C3* C1*
> 4 3 5 11 2 35.3 334.8 35.3 334.8 ; imp C3* C2* O3* C4*
> ....
> 13 3 1 2 1 0.0 1.3 3 0.0 1.3 3 ; dih C1* C2* O2* H8L
> 11 4 3 1 1 0.0 5.9 3 0.0 5.9 3 ; dih C4* C3* C2* O2*
> ....
> I didn't do anything to the "dih" part. Is this correct, with two  
> extra columns representing "multi" for "dih" (3's shown above)?
>

That looks correct.

> Another question is related with this. For the old grompp of 3.2.1,  
> it didn't give any warning about the extra "0"s for the impropers.  
> Does this affect the original MD results by 3.2.1?

No, unless you were doing free energy runs - then it might have had  
an effect, but even in that case it's easy to check - just rerun a  
couple of steps with the new topology and check for differences.

Cheers,

Erik

-----------------------------------------------------------
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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