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Things are a bit confusing here.<br><br>SETTLE versus other constraint algorithm is chosen at the topology level<br>by putting [ settle ] or [ constraints ] sections in your topology.<br>With of the other constraint algorithms (LINCS or SHAKE) is used<br>for the constraints in the [ constraints ] sections is set in the mdp file.<br><br>For future Gromacs versions I would like to have the [ settle ] sections<br>in the water topology replaced with [ constraints ] and let mdrun<br>decide if to use settle.<br>From a user point of view, this will not change much though,<br>since settle is only useful for water and a user (nearly) never<br>writes a topology for water.<br><br>Berk<br><br>> Date: Mon, 7 Sep 2009 18:28:05 +1000<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] using SETTLE for constraints<br>> <br>> Dmitri Dubov wrote:<br>> > Dear GMX'ers,<br>> > <br>> > I am confused with some basic questions about using SETTLE constraining algorithm in gromacs. <br>> > <br>> > 1) This solution of SHAKE is used, particularly, for spc water. So spc.itp file contains the [ settles ] section, and there is no another [ constraints ] within it. But the parameter "constraint-algorithm" in /water/grompp.mdp (see the gromacs native tutorial for spc water simulation) is set to "Lincs". What is the REAL treatment of water constraints in this case?<br>> <br>> GROMACS transparently uses the best constraint algorithm that you allow <br>> it use on a given molecule. The only way you can *not* use constraints <br>> on water with the standard water .itp files is to #define FLEXIBLE, as <br>> you will see in those .itp files. Since settle is specified there it is <br>> used.<br>> <br>> The choice of LINCS or SHAKE pertains only to molecules for which there <br>> is no other constraint option. You can verify this by doing a quick <br>> simulation of pure water specifying either of the above and seeing that <br>> the results are identical. IIRC the .log file makes a note of what <br>> constraints are being used.<br>> <br>> > 2) From manual the run parameter "constraint-algorithm" has only two (LINCS or SHAKE) alternatives. How can I specify the SETTLE using?<br>> <br>> See above. Looking for SETTLE in the manual index would have helped :-)<br>> <br>> Mark<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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