CCL: how to prevent rotational motion in MD simulations



 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"
 <owner-chemistry%%ccl.net> wrote:
 > Sent to CCL by: "Ana Celia Araujo Vila Verde" [avilaverde ..
 > engr.psu.edu]
 > This is a multi-part message in MIME format.
 >
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 > 	charset="iso-8859-1"
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 >
 > 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
 >
 > <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0
 Transitional//EN"><HTML =
 > DIR=3Dltr><HEAD><META HTTP-EQUIV=3D"Content-Type"
 > CONTENT=3D"text/html; =
 > charset=3Diso-8859-1"></HEAD><BODY><DIV><FONT
 face=3D'Arial' =
 > color=3D#000000 size=3D2>Hi all,</FONT></DIV>=0A=
 > <DIV><FONT face=3DArial
 size=3D2></FONT>&nbsp;</DIV>=0A=
 > <DIV><FONT face=3DArial size=3D2>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&nbsp;of
 > =
 > the =0A=
 > molecule, so I'd like to remove the rotational DOF also during the MD
 > =0A=
 > simulation.</FONT></DIV>=0A=
 > <DIV><FONT face=3DArial
 size=3D2></FONT>&nbsp;</DIV>=0A=
 > <DIV><FONT face=3DArial size=3D2>Could anyone point me to
 either an =
 > article =0A=
 > describing an algorithm or to a freely available code that does this?
 > =0A=
 > </FONT></DIV>=0A=
 > <DIV><FONT face=3DArial
 size=3D2></FONT>&nbsp;</DIV>=0A=
 > <DIV><FONT face=3DArial size=3D2>Thank
 you,</FONT></DIV>=0A=
 > <DIV><FONT face=3DArial
 size=3D2></FONT>&nbsp;</DIV>=0A=
 > <DIV><FONT face=3DArial size=3D2>Ana Vila
 Verde</FONT></DIV>=0A=
 > <DIV><FONT face=3DArial
 size=3D2></FONT>&nbsp;</DIV>=0A=
 > <DIV><FONT face=3DArial size=3D2>(Penn State University,
 Department
 > of =
 > Chemical =0A=
 > Engineering)</FONT></DIV></BODY></HTML>
 > ------_=_NextPart_001_01C663C4.24D82D20--
 >
 >
 >
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