[gmx-users] About Physaica Parameter

[vidhya sankar]

Dear Justin & Mark Thank you for your previous reply
 
                                                                            I am doing Simulation of CNT wrapped By Cyclic Peptide in Water For that I have used the Parameters as follows for my production run
ns_type        = grid       
nstlist        = 5           
rlist        = 1.8      
rcoulomb    = 1.2       
vdwtype         = Shift
rvdw        = 1.2    
coulombtype    =  Reaction-Field-zero    
pme_order    = 4         
fourierspacing    = 0.16    
pcoupl        = Parrinello-Rahman    
pcoupltype    = semiisotropic     (Because My  system is Composed of both pure  Hydrophobic(CNT) & Hydrophilic IProtein) part and Immersed in water) 
tau_p        = 2.0                    
ref_p        = 1.0    1.0              
compressibility = 4.5e-5    4.5e-5   

It run well
But How to check is all these parameters are wright or wrong?
Is  Theer is Any thumb rule to Assign parameters ?

Because My system is Composed of both pure  Hydrophobic(CNT) & Hydrophilic IProtein) part and Immersed in water so I have Selected semiisotropic

What are the parameters Should i Concentrate and How to choose its value  carefully & rationally ?