[gmx-users] viscosity

[David]

On Tue, 2004-07-06 at 18:39, parinald at unsl.edu.ar wrote:
> Hello again:
>             I try to calclate viscosity. I done with g_energy and after
> 10ps, in the md.log appears "your box exploting!".
try with Berendsen coupling or without P coupling.

> 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
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++