[gmx-users] viscosity of spc water model

[Ahmet yıldırım]

Any suggestions?


2013/11/20 Ahmet yıldırım <ahmedo047 at gmail.com>

> 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
>



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Ahmet Yıldırım