[gmx-users] protein domain separation

[Vaclav Horacek]

Hi Hazizian,

> 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, 

This also happened to me once, since it can be impossible to correct the trajectory with nojump once the protein goes through the periodic boundaries.

If I recall right, the solution was to use 'comm_mode' and 'comm_grps' in the *.mdp file to ensure that the protein stays in the middle of the cell and does not cross a boundary.

Hope that helped,
Vaclav


--- On Sun, 10/18/09, hazizian <hazizian at razi.tums.ac.ir> wrote:

> From: hazizian <hazizian at razi.tums.ac.ir>
> Subject: [gmx-users] protein domain separation
> To: gmx-users at gromacs.org
> Date: Sunday, October 18, 2009, 7:38 AM
> 
> 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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