[gmx-users] rigid linear molecules

David van der Spoel spoel at xray.bmc.uu.se
Wed Sep 17 17:07:00 CEST 2003

On Wed, 2003-09-17 at 16:58, lulanyuan wrote:
> Hello, everybody.
> I'm wondering whether there's a way to calculate rigid linear molecules using gromacs, for example CO2. I'm simulating a system in the solvent of liquid CO2. Since the EMP2 model for CO2 is a three site linear molecule with partial charges on the three atoms. It's well known Shake is not able to deal with such kind of linear molecule. Previously I used the quaternion agorithm in softerware DLPOLY. But it's much slower than gromacs.
> Does anyone know a way to do it using gromacs?
yes with dummies. this has been discussed before on the list. look for
acetonitril or for dummies (use saerch feature..)

> Thanks a lot!
> Lanyuan Lu 
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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