normal md simulation code

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8 years 2 weeks ago #1140 by dujiangfeng
Replied by dujiangfeng on topic md simulation code

xavier wrote: Ok, what you describe is a bit funky ...

1- the options you show are reasonable. The protein only moving little during 240 ns is a bit strange. You may have used position restrains without noticing! Check out your mdp file and make sure to use the tpr file you think you are using. It is recommended to use different "root" names for the different stages of the simulation. Such as "mini" for minimization, "equil" for equilibration, "run" for the actual run ...

Did you by any chance remove the COM motion of the protein separately from the solvent?


Hi XAvier,

I checked the position restraint again in my md.mdp, but I don't see any restraint there. I did give the unique prefix for each simulation products, and I wrote log file additionally so it is very easy for me to trace back the things what I did.

It is very strange that the system with polarized water (named sysA) and a system with normal water (named sysB) show a big difference in the exactly same simulation codes (PME used). The protein in sysA didn't move anymore during ~240 ns while the protein in sysB binds to membrane directly before ~300 ps.

I didn't remove COM motion of protein from solvent, since the system made by insane.py.

Thank you for your reply,

Jiang.

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8 years 2 weeks ago #1142 by xavier
Replied by xavier on topic md simulation code
Ok, what you might are experiencing is the freezing of the water in the case of the non-polarized one ... you can check visually if your water is freezing. It is obvious from the arrangement of the waters in long arrays ...

In that case you have to replace about 10% of your water in anti-freeze particle.

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8 years 1 week ago #1146 by dujiangfeng
Replied by dujiangfeng on topic md simulation code

xavier wrote: Ok, what you might are experiencing is the freezing of the water in the case of the non-polarized one ... you can check visually if your water is freezing. It is obvious from the arrangement of the waters in long arrays ...

In that case you have to replace about 10% of your water in anti-freeze particle.


The non-polarized waters were not frozen during the simulation, however, I did have one experience once that our my waters were frozen in NVT step. I should have a look at my polarized waters too to see if they are frozen, I will report it to you soon.

I am wondering here, only within "300ps", the protein has been already binding to the '3.5 nm distance' membrane with PME scheme, is it possible?

Thanks,

Jiang.

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8 years 1 week ago #1149 by dujiangfeng
Replied by dujiangfeng on topic md simulation code
Dear Xavier,

Thank you for your suggestion about freeze of the water. After visualizing the system, I am pretty sure that the polarized waters should be frozen since the "V" shape of each water disappeared and every 4-6 waters formed into one smooth line, which I actually noticed at beginning but I thought it was one of the polarized water's properties.

Thank you again,

Jiang.

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