[gmx-users] rigid linear molecules

lulanyuan lulanyuan at sina.com
Wed Sep 17 18:51:02 CEST 2003

Thanks for reply. But after reading the whole discussion of acetonitril, I found that to ajust the moment
of inertia, I have to change the bond length. I think this totally changed the model and will affect the other
parameters in the model(charges and LJ).
Does anyone do things like this kind of mass redistribution in literature? Can anyone
give me some reference for this kind of dummy use?
Thank you.
Lanyuan Lu

----- Original Message -----
From:David van der Spoel <spoel at xray.bmc.uu.se>
To:gmx-users at gromacs.org
Subject:Re: [gmx-users] rigid linear molecules
Date:Wed, 17 Sep 2003 24:03:05 +0800
 >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 
 >> ______________________________________
 >> ===================================================================
 >> £¤4999»ÝÆÕпÓÎÈ˼ÒÓĄ̃ʽ»úÍøÉÏÈÈÂô (http://ad4.sina.com.cn/shc/zhuiyu_hprefresh.html)
 >> _______________________________________________
 >> gmx-users mailing list
 >> gmx-users at gromacs.org
 >> http://www.gromacs.org/mailman/listinfo/gmx-users
 >> Please don't post (un)subscribe requests to the list. Use the 
 >> www interface or send it to gmx-users-request at gromacs.org.
 >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
 >gmx-users mailing list
 >gmx-users at gromacs.org
 >Please don't post (un)subscribe requests to the list. Use the 
 >www interface or send it to gmx-users-request at gromacs.org.
£¤4999»ÝÆÕпÓÎÈ˼ÒÓĄ̃ʽ»úÍøÉÏÈÈÂô (http://ad4.sina.com.cn/shc/zhuiyu_hprefresh.html)

More information about the gromacs.org_gmx-users mailing list