[gmx-users] Position restraint doesn't work

asaraujo at if.sc.usp.br asaraujo at if.sc.usp.br
Fri Dec 31 18:56:00 CET 2004

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

> On Thu, 30 Dec 2004 asaraujo at if.sc.usp.br wrote:
> >
> >Hi All.
> >
> >Well... I thought this was a commom problem but I didn't find anything in
> >search.
> >I want to perform a simulation in a droplet of acetonitrile to calculate
> free
> >energies.
> >The molecules of solvent in the shell of the sphere must to be restrained to
> not
> >fly way to the vacuum.
> >So I changed the resname of these molecules and created another .top file
> and in
> >this topology file I included 3 lines of position restraints(only for the
> >"heavy" atoms C and N):
> >
> >
> >[ position_restraints ]
> >   ai   funct   fc
> >    4      1     1000   1000   1000
> >    5      1     1000   1000   1000
> >    6      1     1000   1000   1000
> >
> >
> >Everything runs fine with grompp and gmxdump (with the lines
> >functype[XXX]=POSRES in it output), but when I run my simulation the shell
> >molecules fly away and Warnings like this:
> >
> >Warning: 1-4 interaction between 1298 and 1303 at distance larger than 5 nm
> Are you sure the posres work? Do you have a posres energy? Is the system
> equilibrated beforehand? You could do this by simulating in a periodic box
> prior to your shell simulation. Is it really necessary to have a droplet?
> --
> 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
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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.
Do you mind anithing that I could do?
Thanks David.

Alexandre Suman de Araujo

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