Restraint in Z direction

[Slimane Doudou]

Dear all,

I was wondering if it is possible to use distance restraints between
two atoms only along Z-direction in PLUMED 1.1.

It is mentioned in the manual that we can use it for position
restraints, but does not say anything for distance restraints.

Thanks,

Slim

[Toni]

I've recently made a patch for this.
If the maintainers agree, perhaps it can be put in the Files section?

Best,
T

[Giovanni Bussi]

Dear Toni,

patches are always welcome! Just send it to this mailing list and all
the interested users will be able to download it.

In case, we will add it to the Files section and, if you agree, to the
next plumed distribution.

Giovanni

[Toni Giorgino]

Dear all,

In case it can be useful, please find a patch to use the projection of a distance (on a cartesian axis or plane) as CV.
It will enable the optional DIR modifier to DISTANCE, with the following syntax:

DISTANCE LIST {group1} {group2} [DIR projection] ...

The modifier [DIR projection] can be DIR followed by X,Y,Z,XY,XZ or YZ.
For instance,

PRINT W_STRIDE 100
DISTANCE LIST 1 2 SIGMA 0.5 DIR X  # projection on X axis
DISTANCE LIST 1 2 DIR Y            # projection on Y axis
DISTANCE LIST 1 2 DIR Z            # projection on Z axis
DISTANCE LIST 1 2 DIR XZ           # projection on XZ plane
DISTANCE LIST 1 2                  # no projection

HILLS HEIGHT 0.1 W_STRIDE 1000
WELLTEMPERED SIMTEMP 300 BIASFACTOR 10
ENDMETA

With the above example, in COLVAR one would therefore find that ...

CV4 ^2 = CV1 ^2  +  CV3 ^2
CV5 ^2 = CV1 ^2  +  CV2 ^2  +  CV3 ^2

Note that it is an experimental feature, so please exercise due caution.

PS. I don't know how google groups handles file attachments. In case it gets removed, I will repost it later.

Best,
Toni


--
Toni Giorgino, PhD - toni.g...@gmail.com - fax +39 0382 1850209
Research Unit on Biomedical Informatics, Barcelona Biomedical Parc (GRIB-IMIM-PRBB, grib.imim.es)

[cui haosheng]

Dear Toni:

I'm wondering if your patch is applying to the center of mass of two groups of atoms?

Best,
Haosheng

[Toni Giorgino]

Dear Haosheng

Yes, supplying groups should work quite like the usual DISTANCE keyword.

Best,
T

[davide branduardi]

Hey Toni,

Thank you very much for sharing your efforts!!!!!

Davide

--
**************************************************************
Davide Branduardi
Post Doc- Computational Chemistry
Drug Discovery and Development
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
Phone: +39 010 71781573              Room: 1/27
Fax:   +39 010 7170187

e-mail:
davide.b...@iit.it
davide.b...@gmail.com

[Slimane Doudou]

Dear Toni,

Many thanks for sharing the patch.

Best,

Slim