[gmx-users] using SETTLE for constraints
gmx3 at hotmail.com
Mon Sep 7 11:28:51 CEST 2009
Things are a bit confusing here.
SETTLE versus other constraint algorithm is chosen at the topology level
by putting [ settle ] or [ constraints ] sections in your topology.
With of the other constraint algorithms (LINCS or SHAKE) is used
for the constraints in the [ constraints ] sections is set in the mdp file.
For future Gromacs versions I would like to have the [ settle ] sections
in the water topology replaced with [ constraints ] and let mdrun
decide if to use settle.
>From a user point of view, this will not change much though,
since settle is only useful for water and a user (nearly) never
writes a topology for water.
> Date: Mon, 7 Sep 2009 18:28:05 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] using SETTLE for constraints
> Dmitri Dubov wrote:
> > Dear GMX'ers,
> > I am confused with some basic questions about using SETTLE constraining algorithm in gromacs.
> > 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?
> GROMACS transparently uses the best constraint algorithm that you allow
> it use on a given molecule. The only way you can *not* use constraints
> on water with the standard water .itp files is to #define FLEXIBLE, as
> you will see in those .itp files. Since settle is specified there it is
> The choice of LINCS or SHAKE pertains only to molecules for which there
> is no other constraint option. You can verify this by doing a quick
> simulation of pure water specifying either of the above and seeing that
> the results are identical. IIRC the .log file makes a note of what
> constraints are being used.
> > 2) From manual the run parameter "constraint-algorithm" has only two (LINCS or SHAKE) alternatives. How can I specify the SETTLE using?
> See above. Looking for SETTLE in the manual index would have helped :-)
> 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