[gmx-users] LINCS WARNING - Protein-Membrane-system

[Shima Arasteh]

Hi,

I have a system of Peptide-popc-ions-water to simulate. I'm trying to run MD simulation following the Justin's tutorial of kalp15-DPPC. 

The force field which I use, is charmm36. 

In NVT step, I get LINCS-warning as follow:
Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2.460224, max 54.696251 (between atoms 4719 and 4716)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.182707, max 15.613569 (between atoms 4725 and 4726)


When I checked the warning, I see the first warning is related to 2 atoms of 71POPC, the chain of 71POPC residue is broken near these two atoms. And the other warning is related to a bond between H and C in the other POPC residue.

Some settings of nvt.mdp is as:
ns_type        = grid        
nstlist        = 5      
rlist        = 1.2        
rlistlong       = 1.4
rcoulomb    = 1.2       
rvdw        = 1.2        
pbc        = xyz   
vdwtype         = switch
rvdw_switch     = 0.8
; Parameters for treating bonded interactions
continuation    = no      
constraint_algorithm = LINCS    
constraints    = all-bonds   
lincs_iter    = 1        
lincs_order    = 4        

Do I need to increase the rlistlong? I have done a simulation of POPC-water before with these settings, but everything was ok. So what's the problem? Anybody may help me?

Your suggestions would be appreciated. Thanks in advance.

 
Sincerely,
Shima