[gmx-users] Protein-POPC-water

[Shima Arasteh]

 Dears,

I am trying to simulate a system of water, POPC and protein using charmm36 ff.
I follow the protocol suggested in KALP15-DPPC tutorial.
I follow the tutorial step by step up to NVT equilibration without any bond or any  other type warnings. 
Then I run the grompp :
  # grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

My nvt.mdp file is as :
define        = -DPOSRES   
; Parameters describing the details of the NVT simulation protocol
integrator    = md     
dt        = 0.002      
nsteps        = 50000   
; Parameters controlling output writing
nstxout        = 1000       
nstvout        = 1000       
nstenergy    = 1000     
nstlog        = 1000        

; Parameters describing neighbors searching and details about interaction calculations
ns_type        = grid     
nstlist        = 5       
rlist        = 1.2       
rlistlong       = 1.4
rcoulomb    = 1.2    
rvdw        = 1.2       
pbc        = xyz        

; Parameters for treating bonded interactions
continuation    = no     
constraint_algorithm = LINCS    
constraints    = all-bonds  
lincs_iter    = 1    
lincs_order    = 4     

; Parameters for treating electrostatic interactions
coulombtype    = PME       
pme_order    = 4     
fourierspacing    = 0.16        

; Temperature coupling parameters
tcoupl        = v-rescale            
tc-grps        = Protein POPC    SOL_CL    ; Define groups to be coupled separately to temperature bath
tau_t        = 0.1    0.1    0.1       
ref_t        = 310     310    310       

; Pressure coupling parameters
pcoupl        = no       

; Miscellaneous control parameters
; Dispersion correction
DispCorr    = EnerPres 
; Initial Velocity Generation
gen_vel        = yes      
gen_temp    = 310      
gen_seed    = -1      
; Centre of mass (COM) motion removal relative to the specified groups
nstcomm        = 1           
comm_mode    = Linear        
comm_grps    = Protein_POPC SOL_CL   



  # mdrun -deffnm nvt -v

In this step, the nvt is not done and what I get is as :
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
step 0Warning: 1-4 interaction between 4707 and 4716 at distance 3.491 which is larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 23534.929688 (between atoms 257 and 258)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 885865856.000000 (between atoms 4521 and 4520)

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 7.158197 (between atoms 3763 and 3765)
   3797   3796   90.0    0.1111   0.2486      0.1111
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 11.492531 (between atoms 3712 and 3710)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4472   4469   39.4    0.1111   0.1029      0.1111
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4471   4469   89.9    0.1111   0.1222      0.1111
    229    231  114.8    0.1756 169.1857      0.1430
    229    230   77.2    0.1053   4.3596      0.0997
   3796   3797   90.0    0.1111   0.2486      0.1111
    231    251  118.0    0.1810 161.6257      0.1490
   3777   3775   52.8    0.1111   0.1136      0.1111
    231    232  166.9    0.1366 138.9714      0.1080
   3776   3775   89.2    0.1111   0.1218      0.1111
    251    252   33.6    0.1300   7.0818      0.123

and finaly some pdb files are printed.
What's the problem? I checked some of atom pairs in this note, however some usual bonds are expected.


Sincerely,
Shima