[gmx-users] mdrun -rerun: bonded interactions of protein

[Justin A. Lemkul]

NG HUI WEN wrote:
> Hi Gmxusers,
> 
>  
> 
> I have been trying to run mdrun –rerun to get the energy of the protein 
> in my protein-lipid system. I know similar questions have been raised on 
> this topic before, I have tried to glean useful information from them to 
> solve my problem but unfortunately to no avail. Thanks for your patience!  
> 
>  

Exactly how would define "the energy of the protein?"  This is a question that 
gets posted very frequently, and the answer is always the same - it doesn't 
correspond to any useful quantity, not that you can extract one, anyway.

As you've noticed, energygrps can only be used to decompose short-range 
nonbonded interactions, not bonded or long-range interactions.  You will have 
energy terms associated with the Coul.-recip. term from PME; how do you deal 
with that?  As you can see, it is not a trivial exercise.

-Justin

> 
> As I did not have energygrps in the initial .mdp file, I included it 
> this time  
> 
>  
> 
> integrator  = md       
> nsteps      = 0  
> dt          = 0.002          
> nstxout     = 50000          
> nstvout     = 50000          
> nstenergy   = 500      
> nstlog      = 500      
> Continuation      = yes      
> constraint_algorithm = lincs 
> constraints = all-bonds
> lincs_iter  = 1        
> lincs_order = 4        
> ns_type           = grid           
> nstlist           = 5        
> 
> rlist       = 1.2      
> rcoulomb    = 1.2      
> rvdw        = 1.2      
> coulombtype = PME      
> pme_order   = 4        
> fourierspacing    = 0.16           
> tcoupl            = Nose-Hoover          
> tc-grps           = Protein POPE    SOL_CL-    
> 
> tau_t       = 0.1 0.1   0.1  
> ref_t       = 323       323   323  
> pcoupl            = Parrinello-Rahman    
> pcoupltype  = semiisotropic        
> 
> tau_p       = 5.0            
> ref_p       = 1.0 1.0        
> compressibility = 4.5e-5      4.5e-5     
> pbc         = xyz      
> DispCorr    = EnerPres 
> gen_vel           = no       
> nstcomm         = 1
> comm-mode       = Linear
> comm-grps       = Protein_POPE SOL_CL-
> *energygrps  = Protein SOL POPE*
> 
>  
> 
> I then did
> 
> 1)grompp –f new.mdp –n index.ndx –c old.tpr –o rerun.tpr –p topol.top
> 
> 2)trjconv –f old.trr –n index.ndx –s rerun.tpr –o rerun.trr (when 
> prompted, I selected “0” system)
> 
> 3)mdrun –s rerun.tpr –rerun rerun.trr
> 
>  
> 
> I notice that the previous post 
> http://oldwww.gromacs.org/pipermail/gmx-users/2009-January/038968.html 
> suggested to use tpbconv (on rerun.tpr) and trjconv (on rerun.trr) to 
> extract the protein only. While it was possible to do so with trjconv, 
> it wasn’t feasible with tpbconv (I’m using gromacs 4.0.7) – I might have 
> missed out something as I did not get any prompt/output (see below)
> 
>  
> 
> tpbconv -s topol.tpr -n index_P.ndx -o rerun2.tpr
> 
>  
> 
> Reading toplogy and shit from topol.tpr
> Reading file topol.tpr, VERSION 4.0.7 (single precision)
> 0 steps (0 ps) remaining from first run.
> You've simulated long enough. Not writing tpr file
> 
>  
> 
> Using the g_energy command on the output energy.edr file, I got among 
> others, these options to choose
> 
> 49  Coul-SR:Protein-Protein             50  
> LJ-SR:Protein-Protein            
> 
> 51  Coul-14:Protein-Protein             52  
> LJ-14:Protein-Protein            
> 
>  
> 
> In order to get the energy of the protein, I reckon I have to add 
> 49,50,51,52 (to account for the nonbonded components) and
> 
> 1  Angle            2  G96Angle         3  Proper-Dih.      4  
> Ryckaert-Bell.  5  Improper-Dih 
> 
> for the bonded components. However, I think 1-5 is the bonded terms for 
> the system and not the protein alone. Can anyone help me with this?
> 
>  
> 
>  
> 
> Also, on a slightly different note, this post 
> http://oldwww.gromacs.org/pipermail/gmx-users/2005-July/016307.html 
> suggested that the force constant of the solvent (DMSO) to be adjusted 
> to zero. Am I right to think that it does not apply to my case as my 
> protein-lipid system is solvated with SPC? (I read that SPC is rigid 
> water. I did not add –DFLEXIBLE in .mdp)
> 
>  
> 
> Any help would be highly appreciated.Thanks!
> 
>  
> 
> HW
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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