[gmx-users] Position restraint doesn't work

asaraujo at if.sc.usp.br asaraujo at if.sc.usp.br
Sun Jan 2 00:39:47 CET 2005

Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> On Fri, 31 Dec 2004 asaraujo at if.sc.usp.br wrote:
> >Yes, It's working. There are the lines functype[XXX]=POSRES in the output of
> >gmxdump and there is the position restraint energy in the .edr file.
> >Before I create my sphere I ran a normal simulation (cubic box, temperature
> and
> >pressure control, pbc, cut-off, etc.) and with the output box I create my
> >sphere.
> >It's necessary to be a sphere because my simulations is with ions and like I
> >read in some paper from Aqvist, in these case the value of calculated free
> >energy depends of the value of the cut-off's and is better to perform the
> >simulation in a sphere in vacuum and out of this sphere use the Born's
> >correction. So, the sphere is necessary.
> >I don't know what is wrong because a friend of mine make simulations in a
> sphere
> >of WATER using postion restraints and it works. In my case I use
> acetonitrile
> >and it doesn't work like I said in the other message.
> The cohesion between acetonitril molecules is far less than between water
> of course. Nevertheless the position restraints should work. Could it
> still be a problem with periodicity?
> --
> 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://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

Yes... the cohesion is smaller in acetonitrile than water, but I don't think
it's SO far... whatever...
What do you mean about the position restraint still be a problem with
periodicity??? Are you suggesting me to aply the position restraint in a box
with periodicity and see if it works? I didn't do this yet, but I'll do...
But..do you agree that position restraint shoul work in my system? Or do you
think that this simulation of a sphere can generate problems???

Alexandre Suman de Araujo

This message was sent using IMP, the Internet Messaging Program.

More information about the gromacs.org_gmx-users mailing list