Aneesh,
I think as a general rule SHAKE cannot handle linear molecules - taking
CO2 as an example, if the C atom wanders out of line the algorithm can't
bring it back into line by applying forces which are aligned along the
direction of the molecule (i.e. the previous perfectly linear
configuration).
As a workaround, it might be possible to SHAKE a fictitious O-O bond,
then connect these with 'normal' bonds to the C (with a sufficiently
high force constant) but this is a bit of a hack.
Steve.
David A. Case wrote:
> On Thu, Oct 16, 2008, aneesh cna wrote:
>
>> I am using Amber 9.0 for simulating a system with 3-site
>> Carbon dioxide. I want to keep Carbon dioxide as rigid molecules through
>> out the simulation. How to do this in Amber? How to mention this in the
>> input file ?
>
> You can use SHAKE to keep the individual molecules rigid. However, please
> check your results carefully: CO2 is a linear molecule that requires special
> attention to keep rigid. I'm not sure whether or not the Amber code as it
> stands is suited to this problem. Maybe someone on the list has tried this.
>
> ...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Fri Oct 17 2008 - 05:10:39 PDT
