[gmx-users] Position restraint doesn't work

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 31 12:38:06 CET 2004

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
>I want to perform a simulation in a droplet of acetonitrile to calculate free
>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 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

More information about the gromacs.org_gmx-users mailing list