[gmx-users] Best way to handle linear rigid molecules.
gmx3 at hotmail.com
Mon Jul 13 14:47:33 CEST 2009
This question has been asked several times before on this list.
The proper way to handle this in Gromacs is to introduce two dummy mass particles
in such a way the total mass and the moment of inertia is identical to CO2.
Then you can construct the positions of the three mass-less C and O atoms from
the positions of the masses using virtual sites (see the manual).
> Date: Fri, 10 Jul 2009 16:58:29 +0100
> From: Jennifer.Williams at ed.ac.uk
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Best way to handle linear rigid molecules.
> Hello users,
> I am using gromacs v 4.0.5
> What is the best way to treat linear triatomic molecules such as CO2.
> Is there some kind of rigid algorthym as in DL_POLY?
> In the asbsence of a ?rigid? algorthym. I initially intended to ?fix?
> the C=O bond length using constraints (as below) and somehow ?fix? the
> O=C=O bond angle to 180.
> [ atomtypes ]
> ; type mass charge ptype c6 c12
> C_CO2 12.01115 0.5406 A 0.0000 0.00000000
> O_CO2 15.9994 -0.2703 A 0.29847 1.10765301
> [ moleculetype ]
> ; name nrexcl
> CO2 2
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> 1 C_CO2 1 CO2 C_CO2 1 0.5406 12.01115
> 2 O_CO2 1 CO2 O_CO2 1 -0.2703 15.9994
> 3 O_CO2 1 CO2 O_CO2 1 -0.2703 15.9994
> [ constraints ]
> ; ai aj funct c0 c1
> 1 2 1 0.12088
> 1 3 1 0.12088
> [ angles ]
> ; ai aj ak funct c0 c1
> 2 1 3 1 180.00
> First question... How do I go about fixing this angle to 180degrees?
> Should I just make c1 extremely large? Is there a more elegant way of
> going about this? Someone also mentioned using a virtual site
> representation for the C. Any comments on this welcome.
> I read some posts which imply that the angle bending code apparently can't
> handle angles of exactly 180 degrees.
> This was a while ago so perhaps this has been dealt with in the
> current version of gromacs?
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Express yourself instantly with MSN Messenger! Download today it's FREE!
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users