[gmx-users] viscosity

[parinald at unsl.edu.ar]

Hello again:
            I try to calclate viscosity. I done with g_energy and after
10ps, in the md.log appears "your box exploting!".
My .mdp file is:


 constraints         =  all-bonds
integrator          =  md
dt                  =  0.001	; ps !
nsteps              =  50000   ; total 50 ps.
nstcomm             =  1
nstxout             =  100
nstvout             =  100
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  simple
coulombtype         =  PME
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  0.9
; Berendsen temperature coupling is on in two groups
Tcoupl              =  nose-hoover
tc-grps             =  Cl-  Na+  DMSO
tau_t               =  0.1	0.1  0.1
ref_t               =  300	300  300
; Energy monitoring
energygrps          =  Cl-  Na+  DMSO
; Isotropic pressure coupling is not on
Pcoupl              =  Parrinello-Rahman
;Pcoupltype         =  isotropic
tau_p               =  1.0
compressibility     =  4.5e-5
ref_p               =  1.0
; Free Energy Perturbacion
;free_energy         =  yes
;init_lambda         =  0
;delta_lambda        =  0.00002
;sc_ alpha           =  0.1
;sc_sigma            =  0.3 ;nm
; Viscosity
acc_grps            =  Cl-                 Na+                DMSO
accelerate          =  0.01  0.0  0.0	 0.01 0.0  0.0	  -0.01  0.0  0.0
cos_acceleration    =  0.6029295
; Dielectric constant
epsilon_r           = 1
; Generate velocites is off at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529