[gmx-users] Re: distance restraints for atoms on 2 chains

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 2 01:32:01 CEST 2011

pdb2gmx -chainsep (-merge in 4.0.x and before) should allow you to create a 
merged [moleculetype] to apply distance restraints.  If you're just trying to 
use a harmonic potential to define some sampling distance (for US), then 
distance restraints are not necessary, just apply the pull code.


Sai Pooja wrote:
> Also, the chains do not diffuse apart in time since they are position 
> restrained(some parts of each chain are ...)
> On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja <saipooja at gmail.com 
> <mailto:saipooja at gmail.com>> wrote:
>     Hi,
>     I have 5 chains in my Protein. I want to apply distance restraints
>     for doing Umbrella Sampling for 2 atoms on different chains. Is
>     there a way to do this since the two chains have separater itp files.
>     Pooja
>     -- 
>     Quaerendo Invenietis-Seek and you shall discover.
> -- 
> Quaerendo Invenietis-Seek and you shall discover.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list