[gmx-users] viscosity of spc water model

[Ahmet yıldırım]

Dear users,

I am trying to get the viscosity (by Einstein relation) of spc water model
(1728 molecules). I tried three Gromacs versions (4.5.4, 4.5.5 and 4.6.4).
But I couldnt get the results in Hess' paper (J. Chem. Phys. 116, 209
(2002)). Whereas I used the same parameters (NVT, Reaction field/PME,
double precisision...) in paper. I also tried different parameters.  I am
always getting a result as the figure (evisco.png ) in vis.tar.gz for all
runs. My input files:
https://www.dropbox.com/s/v2hyr0lqcj4ue78/vis.tar.gz

What do you suggest me?


My commands:

***1.step***
genconf -f spc216.gro -o spc1728_1.gro -nbox 2 2 2
***2.step***
editconf -f spc1728_1.gro -box 3.75 3.75 3.75 -density 980 -o spc1728.gro
************************************EM************************************************************
***2.step***
grompp -v -f em.mdp -c spc1728.gro -p spc.top -o spc-em.tpr
mdrun -v -deffnm spc-em
************************************NVT************************************************************
***3.step***
grompp -v -f nvt.mdp -c spc-em.gro -p spc.top -o spc-NVT.tpr
mdrun -v -deffnm spc-NVT
************************************NPT************************************************************
***4.step***
grompp -v -f npt.mdp -c spc-NVT.gro -p spc.top -o spc-NPT.tpr
mdrun -v -deffnm spc-NPT
************************************RUN*************************************************************
***5.step***
grompp -v -f run.mdp -c spc-NPT.gro -p spc.top -o spc-RUN.tpr
mdrun -v -deffnm spc-RUN

Analysis:
g_energy -f spc-RUN.edr -vis

Thanks in advance

-- 
Ahmet Yıldırım