From owner-chemistry&$at$&ccl.net Thu Apr 20 15:05:00 2006 From: "Konstantin Kudin konstantin_kudin_-_yahoo.com" To: CCL Subject: CCL: how to prevent rotational motion in MD simulations Message-Id: <-31569-060420121849-22428-+TjqmewJBQNzeb9ynCiOgQ{=}server.ccl.net> X-Original-From: Konstantin Kudin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 20 Apr 2006 08:18:41 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Konstantin Kudin [konstantin_kudin-#-yahoo.com] Hi Ana, It appears that you want to use what is known as "Eckart axis conditions". Use this reference to start chasing down relevant papers: http://dx.doi.org/10.1063/1.1929739 Overall, removing rotations during MD is somewhat tricky. Basically, rotations are defined via a reference structure. So if your system deviates too much from this reference structure, then the degrees of freedom you're removing may be quite far from pure rotations for this current structure in your MD. I hope this helps. Konstantin --- "Ana Celia Araujo Vila Verde avilaverde---engr.psu.edu" wrote: > Sent to CCL by: "Ana Celia Araujo Vila Verde" [avilaverde .. > engr.psu.edu] > This is a multi-part message in MIME format. > > ------_=_NextPart_001_01C663C4.24D82D20 > Content-Type: text/plain; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > Hi all, > =20 > I'm doing molecular dynamics simulations of a single polymer chain in > a = > vacuum and the chain is spinning around its centre of mass. The code > I = > use already removes the translation of the centre of mass, but I am = > concerned that too much energy is passed onto the rotational degree > of = > freedom and not enough energy is kept at the vibrational DOFs of the > = > molecule, so I'd like to remove the rotational DOF also during the MD > = > simulation. > =20 > Could anyone point me to either an article describing an algorithm or > to = > a freely available code that does this?=20 > =20 > Thank you, > =20 > Ana Vila Verde > =20 > (Penn State University, Department of Chemical Engineering) > > ------_=_NextPart_001_01C663C4.24D82D20 > Content-Type: text/html; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > DIR=3Dltr> CONTENT=3D"text/html; = > charset=3Diso-8859-1">

color=3D#000000 size=3D2>Hi all,

=0A= >

I'm doing molecular dynamics = > simulations of a =0A= > single polymer chain in a vacuum and the chain is spinning around its > = > centre of =0A= > mass. The code I use already removes the translation of the centre of > = > mass, but =0A= > I am concerned that too much energy is passed onto the rotational > degree = > of =0A= > freedom and not enough energy is kept at the vibrational DOFs of > = > the =0A= > molecule, so I'd like to remove the rotational DOF also during the MD > =0A= > simulation.

=0A= >

Could anyone point me to either an = > article =0A= > describing an algorithm or to a freely available code that does this? > =0A= >

=0A= >

Thank you,

=0A= >

Ana Vila Verde

=0A= >

(Penn State University, Department > of = > Chemical =0A= > Engineering)

> ------_=_NextPart_001_01C663C4.24D82D20-- > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com