[gmx-users] proper mdp options

[Lukas]

Hi all,

I'm doing a simulation on a small protein. The protein is very unstabel in the simulation and the rmsd after ~ 40 ns is already 0.6 nm for the backbone atoms. I am using the gromos force field.
This really makes me wonder if any of the mdp-parameters is very wrong cause the temperature is really low. Probably there is something wrong with the non-bonded interactions?

here are the mdp-options:

cpp                 =  /lib/cpp

constraints         =  all-bonds

integrator          =  md

dt                  =  0.002         ;# ps !

nsteps              =  1000000       ;# total 2 ns

tinit               =  0

 

;# frequency for center of mass motion removal

nstcomm             =  1

 

;# output

nstxout             =  100000

nstxtcout           =  100

xtc_grps            =  PROTEIN       ;# without water

nstvout             =  100000

nstfout             =  100000

nstlog              =  100

nstenergy           =  100

 

energygrps          =  PROTEIN

 

nstlist             =  5

 

ns_type             =  grid

rlist               =  0.8

 

;# non bonded interactions

coulombtype         =  Reaction-Field

epsilon_r           =  54

rcoulomb            =  1.4

vdwtype             =  cut-off

rvdw                =  0.8

 

;# Berendsen temperature coupling is on in two groups

Tcoupl              =  berendsen

tau_t               =  0.1       0.1

tc-grps             =  PROTEIN   SOL

ref_t               =  278       278

 

;# pressure coupling

Pcoupl              =  berendsen

tau_p               =  0.5

compressibility     =  4.5e-5

ref_p               =  1.0




gen_vel             =  yes

gen_temp            =  278

gen_seed            =  -1



 

Thanks a lot in advance. Cheers,

Lukas
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