normal Protein in water using Elnedyn

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10 years 9 months ago #1697 by bt12d026
Replied by bt12d026 on topic Protein in water using Elnedyn
Do you mean generating particular force constant for constrains? can we do that using martinize??

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10 years 9 months ago #1698 by xavier
Replied by xavier on topic Protein in water using Elnedyn
Nope,

1- changing constrains to bonds is Djurre suggestion
2- generating a new topology using martinize but using the original elnedyn: the one with Martini-2.1

bt12d026 wrote: Do you mean generating particular force constant for constrains? can we do that using martinize??

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10 years 9 months ago #1699 by bt12d026
Replied by bt12d026 on topic Protein in water using Elnedyn
Ok got it sir. Thanks for the quick replies. I will try your suggestions and let you know the outcome. Thanks a lot sir.

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10 years 8 months ago #1747 by bt12d026
Replied by bt12d026 on topic Protein in water using Elnedyn
Dear Sir,

I have followed all the suggestions but I couldn't rectify the LINCS warning. So, I have again generated the topology using MARTINI+Elastic network using the options -elastic -ef 500 -el 0.5 -eu 0.9 -ea 0 -ep 0. Now, my system is running without any errors. So,is it fine to use elastic network instead of ElneDyn ff?

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10 years 8 months ago #1748 by xavier
Replied by xavier on topic Protein in water using Elnedyn
The combination of Martini+elastic network should not be far from ElNeDyn but it is a different approach and has not been tested very carefully. You may choose to use it but it is at your own risks.

I am worried that you can not use ElNeDyn ... any clue why?

bt12d026 wrote: Dear Sir,

I have followed all the suggestions but I couldn't rectify the LINCS warning. So, I have again generated the topology using MARTINI+Elastic network using the options -elastic -ef 500 -el 0.5 -eu 0.9 -ea 0 -ep 0. Now, my system is running without any errors. So,is it fine to use elastic network instead of ElneDyn ff?

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10 years 8 months ago #1749 by bt12d026
Replied by bt12d026 on topic Protein in water using Elnedyn
Dear Sir,
Thanks for the prompt reply. I tried all the possible ways to impose ElNeDyn on my protein (like increasing the masses for ring structures from 45 to 72 and switched the backbone constrains into bonds with large (90000) force constant....etc). But my system collapsing with a LINCS warning every time.

Actually there is a problematic HIS residue in my system. When I increase the time step from 1fs to 20fs during equilibration, grompp is notifying me that "The oscillation period of BB and SC1 bond of HIS is 10 times smaller than the time step".

Are there any other ways to try? If you need any files, I am ready to provide sir.

Thank you

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10 years 8 months ago #1750 by xavier
Replied by xavier on topic Protein in water using Elnedyn
How is your HIS defined? In Martini-2.2?

You have a force constant at that location? What is the force constant?

bt12d026 wrote: Dear Sir,
Thanks for the prompt reply. I tried all the possible ways to impose ElNeDyn on my protein (like increasing the masses for ring structures from 45 to 72 and switched the backbone constrains into bonds with large (90000) force constant....etc). But my system collapsing with a LINCS warning every time.

Actually there is a problematic HIS residue in my system. When I increase the time step from 1fs to 20fs during equilibration, grompp is notifying me that "The oscillation period of BB and SC1 bond of HIS is 10 times smaller than the time step".

Are there any other ways to try? If you need any files, I am ready to provide sir.

Thank you

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10 years 8 months ago #1751 by bt12d026
Replied by bt12d026 on topic Protein in water using Elnedyn
The Protein.itp file shows

1036 1037 1 0.19500 94000 ; HIS

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10 years 8 months ago #1752 by bt12d026
Replied by bt12d026 on topic Protein in water using Elnedyn
The HISTIDINE residue is defined as

1036 P5 466 HIS BB 1036 0.0000 ; C
1037 SC4 466 HIS SC1 1037 0.0000 ; C
1038 SP1 466 HIS SC2 1038 0.0000 ; C
1039 SP1 466 HIS SC3 1039 0.0000 ; C

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10 years 8 months ago #1753 by xavier
Replied by xavier on topic Protein in water using Elnedyn
K is way too high! We need to change this!

Try to reduce it to 50000/60000 ...

bt12d026 wrote: The Protein.itp file shows

1036 1037 1 0.19500 94000 ; HIS

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10 years 8 months ago #1754 by bt12d026
Replied by bt12d026 on topic Protein in water using Elnedyn
But all the other HIS also have the same value sir.

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10 years 8 months ago #1755 by xavier
Replied by xavier on topic Protein in water using Elnedyn

bt12d026 wrote: But all the other HIS also have the same value sir.


Change them all ... this force constant is insane! This must be corrected in martinize ... trust me :))

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10 years 8 months ago #1756 by bt12d026
Replied by bt12d026 on topic Protein in water using Elnedyn
Ok sir... I'll change accordingly and get back to you.

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10 years 8 months ago #1757 by bt12d026
Replied by bt12d026 on topic Protein in water using Elnedyn
Sir, now TRP is giving trouble. The K value for TRP is 73000. Shall I change also it to 60000?

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10 years 8 months ago #1758 by xavier
Replied by xavier on topic Protein in water using Elnedyn

bt12d026 wrote: Sir, now TRP is giving trouble. The K value for TRP is 73000. Shall I change also it to 60000?



TRPs should not give troubles! You should make that your system is conformation is fine. Which bond of the TRP is making trouble?

You can try to get K(TRP) down but that is really unusual trouble!

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10 years 8 months ago #1759 by bt12d026
Replied by bt12d026 on topic Protein in water using Elnedyn
The bond between backbone (BB) and side-chain bead (SC1) is giving trouble.

664 665 1 0.25500 73000 ; TRP

When I change K (of TRP) to some 60000, again I am receiving NOTE: The oscillation period of BB and SC1 bond of HIS is 10 times smaller than the time step.

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10 years 8 months ago #1760 by xavier
Replied by xavier on topic Protein in water using Elnedyn

bt12d026 wrote: The bond between backbone (BB) and side-chain bead (SC1) is giving trouble.

664 665 1 0.25500 73000 ; TRP

When I change K (of TRP) to some 60000, again I am receiving NOTE: The oscillation period of BB and SC1 bond of HIS is 10 times smaller than the time step.


The warning is some thing but the stability in the simulation is more important.

You should have the masses of these side chains at 72, a time step of 20 fs, constrains changed to bonds with a 100000/150000 kJ/mil/mn-2 and things should just go smooth ... if not your protein might be tricky but I doubt it.

If things persist I might have a look at your system/topology and give it a try.

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10 years 8 months ago #1766 by bt12d026
Replied by bt12d026 on topic Protein in water using Elnedyn
Dear Sir,

I think the problem has been resolved by following the three recommendations. :)

But I have a small doubt. What if my system has a cholesterol (Which is a ring structure) and the increase in ring structure bead masses...does it show any affect on cholesterol???

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10 years 8 months ago #1767 by xavier
Replied by xavier on topic Protein in water using Elnedyn

bt12d026 wrote: Dear Sir,

I think the problem has been resolved by following the three recommendations. :)

But I have a small doubt. What if my system has a cholesterol (Which is a ring structure) and the increase in ring structure bead masses...does it show any affect on cholesterol???


It might slightly affect the dynamics of the cholesterol but not in a significant manner. You could also change the masses of the side chains directly in the protein itp. Then the cholesterol would not be affected.

For the record coul you list the changes you performed. That might be helpful for other users and refinement of the FF.

Thank you.

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10 years 8 months ago #1768 by bt12d026
Replied by bt12d026 on topic Protein in water using Elnedyn
Dear Sir,

Here are the modifications I have done for my ElNeDyN system.

1) Reduced the Force constant for HIS residue from 94000 to 60000 KJ/mol-1nm-2
2) Adjusted the masses of ring structure's side chain beads (3:1 or 2:1 mapping) to 72
3) Converted the constraints between backbone beads (in the section [constraints]) to bonds with a high force constant. The block of backbone-backbone constraints has been shifted to the [bonds] section and appended a column containing force constants, ~90000 kJ/mol.

Thanks a lot sir for spending your valuable time for me :)

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