normal How important is nstlist=1, instead of nstlist=10?

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10 years 4 months ago - 10 years 4 months ago #2676 by Rajat Desikan
Hi
This paper talks about artificial flux of water molecules arising from erroneous .mdp options in gromacs, especially in protein-membrane systems.

pubs.acs.org/doi/abs/10.1021/ct3001359

How important are these effects in Martini FF? Especially nstlist and electrostatics? Have you guys done any tests? I have a membrane-protein channel system, and do not want a water flux inside the channel if I can help it!

Thanks,
Last edit: 10 years 4 months ago by Rajat Desikan.

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10 years 4 months ago #2792 by xavier
We have not tested these parameters but it would be nice to do … if you like to do so and post the results back this would be greatly appreciated.

XAvier.

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10 years 4 months ago #2793 by Rajat Desikan
Replied by Rajat Desikan on topic How important is nstlist=1, instead of nstlist=10?
Hi Xavier,
How long do you think the test simulations need to be? 200 ns? The atomistic simulations were run for 100 ns.

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10 years 4 months ago #2794 by xavier
I have not read the paper yet, but I'd guess tat you can run much longer simulations time than at the atomistic level. 200 ns is a good start but you could go longer.

One point you have to keep in mind is that the CG water is larger than atomistic one since it represents 4 real water molecules. The transfer of CG water through pore might thus be more difficult.

Rajat Desikan wrote: Hi Xavier,
How long do you think the test simulations need to be? 200 ns? The atomistic simulations were run for 100 ns.

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10 years 4 months ago #2818 by Rajat Desikan
Replied by Rajat Desikan on topic How important is nstlist=1, instead of nstlist=10?
Hi Xavier,
The flux of water is through the protein channel itself which is atleast 3 nm in dia. So, that could be an issue in Martini. However, I do not think that this flux will affect the protein structure. Your comments on this?

I will carry out 500 ns comparitive runs and tell you (because with nstlist = 1, I only get 80 ns/day on 64 procs...My system is approximately 150000 Martini atoms)...I will need some time for this...Expect an update by early December 2013...

Any idea about gromacs tools to calculate water flux?

Thanks...

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10 years 4 months ago #2894 by xavier
Hi Rajat,

3 nm is pretty large. You should see water beads going through.

There are no g_tool for the flux I believe. Someone tried to get one working in the lab but it was not straight forward to get it to work properly. The periodic boundary conditions seem to make life a bit difficult. The water bead move relatively fast it might be an issue to know how a particular bead goes from one side to the other: through the bilayer/channel or the PBC. Another issue I could remember was to differentiate a water bead going through the channel or the bilayer it self.

If you get something tho work we'll be happy to test it and put it on the web.

XAvier.

Rajat Desikan wrote: Hi Xavier,
The flux of water is through the protein channel itself which is atleast 3 nm in dia. So, that could be an issue in Martini. However, I do not think that this flux will affect the protein structure. Your comments on this?

I will carry out 500 ns comparitive runs and tell you (because with nstlist = 1, I only get 80 ns/day on 64 procs...My system is approximately 150000 Martini atoms)...I will need some time for this...Expect an update by early December 2013...

Any idea about gromacs tools to calculate water flux?

Thanks...

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10 years 4 months ago #2929 by siewert
You may want to contact one of my post-docs, Manuel Melo (This email address is being protected from spambots. You need JavaScript enabled to view it.), he has a tool to calculate the flux through a membrane channel ...

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