[gmx-users] About frozen groups

Mohammed Kamal mohkam978 at hotmail.com
Tue Jan 20 05:54:16 CET 2009

Sorry if this mail was duplicated... I think I have sent it by error to gmx-usres-requsts at gromacs.org
Dear Gromacs community,
I’m running MD simulation for ligand-enzyme complex with the help of the great tutorial set by Kerrigan using version 3.3.1.
In certain stage of my simulation I need to fix the position of some residues in the enzyme. In order to do so I thought about two options for doing that:

The first is by the use of “freezegrps” where I have generated and .ndx (IRS.ndx) file for the residues to be frozen and I have modified my .mdp file to be:
title                    = dynamic for 2zd1
cpp                      = /usr/bin/cpp
integrator               = md
constraints              = none
dt                       = 0.002
nsteps                   = 500000  ; total 1 ns.
nstcomm                  = 1
nstxout                  = 5000
nstvout                  = 0
nstfout                  = 0
nstlist                  = 10
ns_type                  = grid
rlist                    = 1
coulombtype              = PME
rcoulomb                 = 1
vdwtype                  = cut-off
rvdw                     = 1.4
fourierspacing           = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
pme_order                = 6
ewald_rtol               = 1e-5
optimize_fft             = yes
Tcoupl                   = berendsen
tau_t                    = 0.1 0.1 0.1 0.1
tc_grps                  = protein T27 SOL Cl ; T27 is the ligand
ref_t                    = 300 300 300 300
energygrps               = protein T27 SOL 
energygrp_excl           = IRS IRS IRS SOL
freezegrps               = IRS
freezedim                = Y Y Y
Pcoupl                   = berendsen
pcoupltype               = isotropic
tau_p                    = 0.5
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529
and when I used the grommp line of 
grompp -f md.mdp -c 2zd1_eq.gro -p 2zd1.top -n IRS.ndx -o md.tpr
I had (as expected) an error massage states that IRS is not an energy group however if I have added IRS as an energy group I had an error that some atoms are in multiple energy Mon. groups.
So, my first question is how to deal with that problem for including my frozen residues that way?
2. The second method I think about is to just position-restrained these residues where I have created an .itp file for the residues need to be fixed (POSRE_IRS.itp) using genpr command. But I don’t know how to consider that in the calculations…. 
Can I just include this file in the toplogy file (#include “POSRE_IRS.itp”) and add the line Define = -DPOSRE_IRS in my .mdp file??
Looking forward for your kind suggestions and comments
Great Thanks

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