[gmx-users] position restraints

[David van der Spoel]

David Mobley wrote:
> David,
> 
> OK, I am running MD using position restraints, and I don't get a
> separate energy output for "restraint energy" or some such; as far as
> I can tell the energy of the restraints is grouped in with the total
> potential energy and never reported separately. I would like it to be
> reported separately, as well (perhaps in the .ene file). Is there a
> way I can get this?

Then you probably have the restraints turned off... Check the tpr file 
for POSRES. This is what the lg file looks like:

    Energies (kJ/mol)
           Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
     9.19554e+02    7.74471e+02    3.96929e+02    5.57953e+02    1.76611e+03
         LJ (SR)   Coulomb (SR) Position Rest.      Potential    Kinetic En.
     4.30246e+04   -2.93575e+05    1.04936e+02   -2.46031e+05    4.66229e+04
    Total Energy    Temperature Pressure (bar)
    -1.99408e+05    3.04983e+02   -1.90371e+02

> 
> Thanks,
> David
> 
> 
> On 5/11/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 
>> David Mobley wrote:
>> > Dear all,
>> >
>> > I'm trying to figure out if there is currently a way to calculate the
>> > position restraint energy (for example, if I'm using a posre.itp file
>> > to  harmonically restrain some atoms) on the fly. Can anyone give me
>> > some pointers? I haven't turned up anything useful on this since 2001
>> > on the mailing list.
>> >
>> > In particular, I would *very much* like to be able to somehow get the
>> > position restraint energy without having to save trajectory snapshots
>> > and reprocess the trajectory somehow, as I need to get the position
>> > restraint energy every 0.2 ps or so over fairly long trajectories, and
>> > I would rather not have to save trajectory snapshots this often to
>> > disk.
>> >
>> > Will I have to modify the code to get this, or is there something more
>> > straightforward I can do?
>>
>> It's not entirely clear to me what you want. If you apply position
>> restraints you get the energy.
>> Where's the problem?
>> >
>> > Thanks,
>> > David
>> > _______________________________________________
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>>
>> -- 
>> David.
>> ________________________________________________________________________
>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,          75124 Uppsala, Sweden
>> phone:  46 18 471 4205          fax: 46 18 511 755
>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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