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

NG HUI WEN HuiWen.Ng at nottingham.edu.my
Wed Nov 10 13:29:15 CET 2010

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


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
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
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!



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