[gmx-developers] multiplicity check on proper dihedral

[Erik Lindahl]

Hi,

Perhaps we should simply change the check to just disallow negative  
and non-integer values.

Cheers,

Erik

On Oct 20, 2008, at 8:37 AM, David van der Spoel wrote:

> Tim Sirk wrote:
>> Hello,
>> I've been using 3.3.3, and after updating to 4.0 RC4 I found that  
>> grompp doesn't
>> accept a proper dihedral with a multiplicity of zero. grompp  
>> returns this error:
>> Value of 'multiplicity' in Proper Dih. is 0, which is smaller than  
>> the minimum
>> of 1
>> I understand that mult=0 probably isn't expected, but it is part of  
>> a forcefield
>> (see below) that I've used with 3.3.3 and I'd like to continue  
>> using it. Might a
>> warning be sufficient, instead of a fatal error? Any input on a  
>> workaround would
>> be appreciated.
>
> A simple workaround would be to rewrite your potential as a ryckaert- 
> bellemans, as you essentially do have a cosine series, please note  
> that RB uses the polymer convention (adding 180 to your angle).
> Indeed your usage seems to completely legitimate, and that was  
> probably overlooked by the person implementing this check . In  
> principle you could remove the check from grompp as well. Note  
> however that adding a constant term to a potential has no effect on  
> the dynamics and relative energies, and hence you might also just  
> leave it out altogether.
>> ; CH1-CH1-CH2-CH2  =>  C22-C23-C24=C25
>>    25   24    23    22     1  0.000       7.47     1
>>    25   24    23    22     1  0.000       3.9      2
>>    25   24    23    22     1  180.000     1.1      3
>>    25   24    23    22     1  0.000      -2.8425   0
>> ; CH1-CH1-CH2-CH2  =>  C24=C25-C26-C27
>>    27   26    25    24     1  0.000       7.47     1
>>    27   26    25    24     1  0.000       3.9      2
>>    27   26    25    24     1  180.000     1.1      3
>>    27   26    25    24     1  0.000      -2.8425   0
>> Thanks.
>> Tim Sirk
>> 12C Randolph Hall
>> Graduate Research Assistant
>> Mechanical Engineering Dept
>> Virginia Tech
>> _______________________________________________
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the www  
>> interface or send it to gmx-developers-request at gromacs.org.
>
>
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala  
> University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www  
> interface or send it to gmx-developers-request at gromacs.org.