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Did not converge to Fmax less than 10
- dariush
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10 years 9 months ago #1728
by dariush
Did not converge to Fmax less than 10 was created by dariush
Hello all,
I have used previously martinize.py several times without elastic network constrains and I did not have problem. Now, I tried it and used several options, but I got "did not converge to Fmax < 10" error.
I know it comes from constrains. Could you please let me know how can I minimize the structure?
I used "steep" and "cg" integrators; did not work.
Or please give me the em.mdp that you are using generally.
Thanks,
Dariush
I have used previously martinize.py several times without elastic network constrains and I did not have problem. Now, I tried it and used several options, but I got "did not converge to Fmax < 10" error.
I know it comes from constrains. Could you please let me know how can I minimize the structure?
I used "steep" and "cg" integrators; did not work.
Or please give me the em.mdp that you are using generally.
Thanks,
Dariush
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- Clement
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10 years 9 months ago #1729
by Clement
Replied by Clement on topic Did not converge to Fmax less than 10
What's the initial force of your minimization? The very first line, step 0. If it's something like "NaN", try to use the double precision version of mdrun (you certainly have to recompile GROMACS with the --enable-double option).
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- xavier
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10 years 9 months ago #1732
by xavier
Replied by xavier on topic Did not converge to Fmax less than 10
Before installing the double precision gromacs version (it has never been necessary for a CG noel), please check the reason of observation.
Typically you system might not have issues ...
Detail the symptoms if you want.
Typically you system might not have issues ...
Detail the symptoms if you want.
Clement wrote: What's the initial force of your minimization? The very first line, step 0. If it's something like "NaN", try to use the double precision version of mdrun (you certainly have to recompile GROMACS with the --enable-double option).
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- dariush
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10 years 9 months ago #1737
by dariush
Replied by dariush on topic Did not converge to Fmax less than 10
As I mentioned I have a protein in my system that during minimization some beads cannot reach to Fmax <10.
If I continue for next step, like equilibration, I will get "Segmentation fault".
It means when I have force on a atom more than 10 (e.g. 100 or 200) then system will will explode in later steps.
I want to know what should be the parameters or options to push system to reach Fmax <10.
I use "em.mdp" file that I could find in tutorials in MARTINI website.
Thanks,
Dariush
If I continue for next step, like equilibration, I will get "Segmentation fault".
It means when I have force on a atom more than 10 (e.g. 100 or 200) then system will will explode in later steps.
I want to know what should be the parameters or options to push system to reach Fmax <10.
I use "em.mdp" file that I could find in tutorials in MARTINI website.
Thanks,
Dariush
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- Clement
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10 years 9 months ago #1738
by Clement
Replied by Clement on topic Did not converge to Fmax less than 10
How many steps of minimization?
What are the first/last forces (Fmax) of the minimization run?
How big is your system, and what does it contain (protein in water, bilayer, ...)?
How/with what tool(s) did you build it?
Did you look at your conformation, as in: what is exploding when you switch to the md (I assume) integrator?
What are the first/last forces (Fmax) of the minimization run?
How big is your system, and what does it contain (protein in water, bilayer, ...)?
How/with what tool(s) did you build it?
Did you look at your conformation, as in: what is exploding when you switch to the md (I assume) integrator?
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- dariush
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10 years 9 months ago #1786
by dariush
Replied by dariush on topic Did not converge to Fmax less than 10
problem solved.
However, for your information, I run minimization several times and Fmax decreased in each time. Then, when I went to next step (NVT) system did not explode anymore.
My system contains bilayer+protein+W and ions.
Thanks,
Dariush
However, for your information, I run minimization several times and Fmax decreased in each time. Then, when I went to next step (NVT) system did not explode anymore.
My system contains bilayer+protein+W and ions.
Thanks,
Dariush
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- xavier
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10 years 9 months ago #1788
by xavier
Replied by xavier on topic Did not converge to Fmax less than 10
That's good news!
I would still try to identify the atoms/molecule and the area that were problematic. You may have created a strange starting conformation that the system had trouble to deal with.
I would still try to identify the atoms/molecule and the area that were problematic. You may have created a strange starting conformation that the system had trouble to deal with.
dariush wrote: problem solved.
However, for your information, I run minimization several times and Fmax decreased in each time. Then, when I went to next step (NVT) system did not explode anymore.
My system contains bilayer+protein+W and ions.
Thanks,
Dariush
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