[gmx-users] Position restraint doesn't work
David van der Spoel
spoel at xray.bmc.uu.se
Sat Jan 1 11:22:21 CET 2005
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
>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 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
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