Viscosity calculation by gmx tcaf

User discussions
1

Dear all users, I am trying to reproduce the viscosity coefficient from gmx tcaf command for bulk waters by taking spc/e water models. But the value at (k=0) is 4.33 cP wheras in literature it is 0.729 cP. Can anyone suggest me anything precaution I should take during the tcaf calculation.

Thank you for any suggestions
Santanu

2

Hi,
a general precaution is to make sure to write coordinates and velocities often enough. The initial, non-exponential, part of the autocorrelation function is very important for obtaining a good fit. If you have a cubic box, you can use option -oc

see also

Best regards
Alessandra

3

Hi.

First of all, sorry it “raising a thread from the dead” is against the forum rules: I really don’t know if there is any policy for that, and it seemed right to ask in here instead of opening a new thread.

I’m trying to use gmx tcaf to calculate the viscosity of ionic liquids. I know that static and non-polarizable charge models will not be enough for a proper result, however I still think there is some issue in my procedures.

I’m using -oc with my 1000 ion pairs cubic boxes. I’m saving the coordinates, velocities and forces at each time step, and I’m simulating with a time step length of 1fs.

My issue is that no matter what I do and besides changing the cations and anions in such a way that their sizes differs by a lot, all simulations indicate that all ionic liquids should have around 2-4 cP.

I’m not concerned on the values, but on the lack of trends, since the measurements should indicate a range from 20 to 200 cP in my tested ionic liquids accordingly to the choice of cations and anions. Not finding any trend is what is really bothering me!

I tested both with and without the “-mol” flag. In both cases also tested with and without an index file that only have one group, [molecules], ranging from 1 to 2000 (that is what I could gather from the manual instruction “With option -mol , the transverse current is determined of molecules instead of atoms. In this case, the index group should consist of molecule numbers instead of atom numbers”), but in reality I’m not quite certain about the file format. Mostly I’m using the flag “-k34” in order to try to improve the final results.

Does anybody has any clues on how to improve my results? Anything that would have close resemblance to a “tutorial” on this specific tool would be realy great…

Thanks a lot in advance!

Yours sincerely,

Jones