Erik Marklund wrote: > Mark Abraham skrev: >> Darrell Koskinen wrote: >>> Hi Tsjerk, >>> So then, if I understand correctly, setting "constraints = >>> all-bonds" is not as realistic as setting "constraints = none", >>> since the latter will allow for flexible (e.g. harmonic) behavoir >>> which is more realistic than fixing the bond to a certain distance, >>> correct? >> >> Actually not. It would be a better model of a harmonic potential >> (duh), but it has been shown that the use of constraints can lead to >> a (more?) acceptable model of a real system, and they allow a larger >> integration time to boot. Check out the papers for the constraint >> algorithms (refs in GROMACS manual). >> >> Mark >> > Agreed. And this is especially true for hydrogen atoms as I understand > it, since their behaviour as quantum particles deviate more from a > classical treatment than is the case for heavier nuclei. This is > mentioned in the gromacs manual. > > /Erik This depends on the system you study. In some cases it is necessary not to constrain the hydrogen atoms to get a better agreement with the experiment. Also, if one needs to deal with vibrational spectra involving hydrogens, they must be mobile.
Ran. >>>> Date: Wed, 11 Nov 2009 21:45:44 +0100 >>>> From: Tsjerk Wassenaar <tsje...@gmail.com> >>>> Subject: Re: [gmx-users] Constraints & Restraints >>>> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>>> Message-ID: >>>> <8ff898150911111245u63c6aa65sa839f24634352...@mail.gmail.com> >>>> Content-Type: text/plain; charset=ISO-8859-1 >>>> >>>> Hi Darrell, >>>> >>>> Constraints and restraints also apply to relative positions. A bond >>>> constraint fixes the bond to a certain distance. constraints = >>>> all-bonds means that all bonds are to be converted to constraints, >>>> rather than have them flexible, e.g. harmonic. Harmonic bonds are >>>> actually more like restraints, penalizing deviations from the >>>> equilibrium values. These equilibrium values and the 'penalty >>>> function' are described in the force field. >>>> >>>> Hope it helps, >>>> >>>> Tsjerk >>>> >>>> On Wed, Nov 11, 2009 at 9:32 PM, <darre...@ece.ubc.ca> wrote: >>>> >>>>> Hi, >>>>> I just have a quick question on contraints and restraints. My >>>>> understanding is that "constraints" fix the position of an atom in >>>>> space and "restraints" restrain the deviation of the atom's position >>>>> from its equilibrium point. Is that correct? If so, then I am a >>>>> little >>>>> confused by the purpose of "constraints = all-bonds" or "constraints >>>>> = none" in an mdp file, since by selection of a force field, which >>>>> has >>>>> bond/angle/dihedral stretching/bending/torsion constants, we are >>>>> specifying the constraints applied to the simulation. So then what is >>>>> the purpose of "constraints = all-bonds" and "constraints = none"? >>>>> >>>>> Thanks. >>>>> >>>>> Darrell >>>>> > > -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355559 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman ------------------------------------------------------ -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php