[gmx-users] Position Restrain

[pandeyprithviraj at gmail.com]

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.......



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
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