[gmx-users] Position Restrain

[Mark Abraham]

pandeyprithviraj at gmail.com wrote:
> Dear all,
> 
> I am trying to put a chain of polyleucine in water - hexane interface. 
> Now after putting the chain of the peptide there are some overlaps. To 
> get rid of those overlaps I tried to run a MD with the position of 
> polyleucine constant (or restrained). But during energy minimization the 
> polyleucine is coming out of the interface. I generated the posre.itp 
> file with "genrestr" command and defined position restrain in the en.mdp 
> file. My en.mdp file is as follows.......

You are almost certainly seeing an artefact of periodic boundary 
conditions. If not, please describe your observations more fully (e.g. 
pictures) - "coming out of the interface" is quite vague. See 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark

> cpp = /lib/cpp
> ;include = -I posre.itp
> define = -DPOSRES
> 
> ; RUN CONTROL PARAMETERS =
> integrator = steep
> ; start time and timestep in ps =
> tinit = 0
> dt = 0.001
> nsteps = 10000
> 
> ; ENERGY MINIMIZATION OPTIONS =
> emtol = 0.00001
> emstep = 0.1
> nstcgsteep = 1000
> 
> and also posre.itp is included in the topology as follows
> 
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> 
> I dont want the polyleucine to come out of the interface. Please help.
> 
> Happy New Year to you all.
> 
> Prithvi
>