[gmx-users] protein domain separation

[hazizian]

Hi
I have done md simulation of a 2-domain protein in water, in 50 K but every 
time I did it these domains are separated from each other, and dont correct 
when I do trjconv -pbc nojump, 
previous time when I did em or pr by doing trjconv -pbc nojump, it 
corrected.

The 50.mdp file is:
title               =  n.pdb
cpp                 =  /lib/cpp
constraints         =  none
integrator          =  md 
dt                  =  0.001
nsteps              =  100000
constraint_algorithm  = shake
shake_tol           = 0.0001
nstcomm             =  1
comm_mode           =  Angular
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.2
coulombtype         =  PME
rcoulomb            =  1.2
rvdw                =  1.4
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  4
ewald_rtol          =  1e-5
optimize_fft        =  yes
 


; Berendsen temperature coupling is on in three groups
Tcoupl              =  berendsen
tau_t               =  0.4       0.4      
tc-grps		    =  protein  non-protein         
ref_t               =  50         50        
; Pressure coupling is  on
Pcoupl              =  berendsen 
tau_p               =  2
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 50 K.
gen_vel             =  yes
gen_temp            =  50.0
gen_seed            =  173529       

are they realy separated or I should do a command to correct it, I search in 
mailing list and could not find the result, please guide me, thank you in 
advance.
 
--
Tehran University of Medical Sciences
www.tums.ac.ir


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