On 27/02/2012 8:35 PM, James Starlight wrote:
Mark,
I've found a possible sollution to restrict oxygens of my X-ray water
by possible plasing the below string in the TOPOLOGY.top of my system
; Include X-ray water topology
#include "XW.itp"
; Include Position restraint file
#ifdef POSRES_XW
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
I havent recieved any errors from gromp. Does this aproach correct in
general ?
Yes. There's only one heavy atom in a water, so that's all you need to
restrain. You want it to have rotational freedom for EM, of course.
I dont know why but after minimisation constrained mollecules were
diffused from the protein interious so POSRES have not worked :(
That's sterically impossible with or without position restraints. Either
you're looking at the wrong before-and-after files, or the after file
has some periodicity artefact in your viewing program. If you set
nstxout = 1 then you can watch the EM process step by step.
My minim.mdp consist of two separate posres for water as well as for
ligand groups ( there are no posre for protein).
define = -DPOSRES_LIG -DPOSRES_XW ; position restrain the
protein
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1000.0 ; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization)
steps to perform
energygrps = Protein CAR
What should I add to that file to activate posres?
Finally are the constraints algorithm needed here ?
James
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
