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Hi,<br><br>This question has been asked several times before on this list.<br>The proper way to handle this in Gromacs is to introduce two dummy mass particles<br>in such a way the total mass and the moment of inertia is identical to CO2.<br>Then you can construct the positions of the three mass-less C and O atoms from<br>the positions of the masses using virtual sites (see the manual).<br><br>Berk<br><br>> Date: Fri, 10 Jul 2009 16:58:29 +0100<br>> From: Jennifer.Williams@ed.ac.uk<br>> To: gmx-users@gromacs.org<br>> CC: <br>> Subject: [gmx-users] Best way to handle linear rigid molecules.<br>> <br>> Hello users,<br>> <br>> I am using gromacs v 4.0.5<br>> <br>> What is the best way to treat linear triatomic molecules such as CO2. <br>> Is there some kind of rigid algorthym as in DL_POLY?<br>> <br>> In the asbsence of a ?rigid? algorthym. I initially intended to ?fix? <br>> the C=O bond length using constraints (as below) and somehow ?fix? the <br>> O=C=O bond angle to 180.<br>> <br>> <br>> [ atomtypes ]<br>> ; type mass charge ptype c6 c12<br>> C_CO2 12.01115 0.5406 A 0.0000 0.00000000<br>> O_CO2 15.9994 -0.2703 A 0.29847 1.10765301<br>> <br>> [ moleculetype ]<br>> ; name nrexcl<br>> CO2 2<br>> <br>> [ atoms ]<br>> ; nr type resnr residu atom cgnr charge mass<br>> 1 C_CO2 1 CO2 C_CO2 1 0.5406 12.01115<br>> 2 O_CO2 1 CO2 O_CO2 1 -0.2703 15.9994<br>> 3 O_CO2 1 CO2 O_CO2 1 -0.2703 15.9994<br>> <br>> [ constraints ]<br>> ; ai aj funct c0 c1<br>> 1 2 1 0.12088<br>> 1 3 1 0.12088<br>> <br>> [ angles ]<br>> ; ai aj ak funct c0 c1<br>> 2 1 3 1 180.00<br>> <br>> First question... How do I go about fixing this angle to 180degrees? <br>> Should I just make c1 extremely large? Is there a more elegant way of <br>> going about this? Someone also mentioned using a virtual site <br>> representation for the C. Any comments on this welcome.<br>> <br>> I read some posts which imply that the angle bending code apparently can't<br>> handle angles of exactly 180 degrees.<br>> <br>> http://www.mail-archive.com/gmx-users@gromacs.org/msg09979.html<br>> <br>> This was a while ago so perhaps this has been dealt with in the <br>> current version of gromacs?<br>> <br>> <br>> Thanks<br>> <br>> <br>> -- <br>> The University of Edinburgh is a charitable body, registered in<br>> Scotland, with registration number SC005336.<br>> <br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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