[gmx-users] protein domain separation

[Justin A. Lemkul]

Vaclav Horacek wrote:
> 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.
> 

Using comm_grps other than "System" for a protein in water can lead to spurious 
collisions and is not appropriate.  Using trjconv is the proper way to fix this 
issue.  If -pbc nojump does not work, another option likely will.  For me -pbc 
mol -ur compact (and/or -center on the protein) works every time.

-Justin

> 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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> 
> 
>       
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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