[gmx-users] a huge topology parameter c1 (angles)

[David van der Spoel]

Mark Abraham wrote:
> Egidijus Kuprusevicius wrote:
>> Dear users,
>>
>> from PRODRG beta server I have got a very big c1 parameter in my 
>> topology file is that normal or smth is wrong with my topology?
>>
>>  
>>
>> [ angles ]
>>
>> ; ai aj ak fu c0, c1, ...
>>
>> ....
>>
>> 17 19 21 2 120.0 505.0 120.0 505.0 ; CAH CAD CAP
>>
>> 20 19 21 2 120.0 505.0 120.0 505.0 ; HAD CAD CAP
>>
>> 19 21 22 2 120.0 560.0 120.0 560.0 ; CAD CAP CAC
>>
>> 19 21 24 2 120.0 560.0 120.0 560.0 ; CAD CAP CAE
>>
>> 22 21 24 2 120.0 *560.0* 120.0 *560.0* ; CAC CAP CAE
>>
>> 21 22 23 2 180.0 *41840001.2* 180.0 *41840001.2 ;* CAP CAC NAB
>>
>> 21 24 25 2 120.0 *505.0* 120.0 *505.0 ;* CAP CAE HAE
>>
>> 21 24 26 2 120.0 505.0 120.0 505.0 ; CAP CAE CAI
>>
>> 25 24 26 2 120.0 505.0 120.0 505.0 ; HAE CAE CAI
>>
>> 16 26 24 2 120.0 505.0 120.0 505.0 ; CAR CAI CAE
> 
> You'll notice that this angle is linear - angle 180 degrees. (If you 
> don't know how to read these lines, consult the table in Chapter 5 of 
> the manual.) A large force constant would prevent any deviation from 
> linear, which I can imagine is right for some weirder chemical species.
> 

An angle of 180 is ill defined, that is, the force is undefined. The 
energy will be fine. Using a large force constant will make certain that 
your system crashes. You should consider using virtual sites instead.

> Mark
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-- 
David van der Spoel, Ph.D.
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