normal How do I know if the coarse-grained (CG) ions are added?

  • lanselibai
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1 week 6 days ago #8023 by lanselibai
I use these two lines to neutralise the system

$ gmx grompp -f minimization.mdp -r system-solvated.gro -c system-solvated.gro -p system.top -o system_genion.tpr
$ echo W | gmx genion -s system_genion.tpr -o system_genion.gro -p system.top -pname NA -nname CL -neutral -conc 0.2

(#include "martini_v2.0_ions.itp") is shown in the system.top file. However, I found out that the above two lines could still work after removing the (#include "martini_v2.0_ions.itp"). Also, I can change "NA" and "CL" to any other names without any errors.

So how the CG ions are reflected in the CG system? I think the CG ions are different from the all-atom ions, right?

Thank you!

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1 week 5 days ago #8024 by Pim
Hello,

Your input lines are correct. You have to follow it up with another grompp command before you can run your minimization though, i.e.

$ gmx grompp -f minimization.mdp -r system-genion.gro -c system-genion.gro -p system.top -o system_minimization.tpr
$ gmx mdrun -v -deffnm system_minimization

Gromacs doesn't use martini_v2.0_ions.itp until you grompp the output of the 2nd line again for your minimization run. If you remove this line, if you don't have the file present in the directory, or have strange atom names, it will complain at the first of these two steps.

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1 week 4 days ago #8030 by lanselibai
Hi Pim,

Thank you! That makes sense to me now.

Can I clarify, should we use "NA+" or "NA"?

In this link
cgmartini.nl/index.php/force-field-parameters/ions
The Na and Cl ions are shown as:

[moleculetype]
NA+ 1
[atoms]
1 Qd 1 ION NA+ 1 1.0
[moleculetype]
CL- 1
[atoms]
1 Qa 1 ION CL- 1 -1.0

So I think I should use "NA+" and "CL-":
$ echo W | gmx genion -s system_genion.tpr -o system_genion.gro -p system.top -pname NA+ -nname CL- -neutral -conc 0.2

However, in the "system_genion.gro" file, it is shown as:
61326NA+ NA70524 2.333 1.929 2.965
My understanding is, this means the residue name is "NA+" while the atom name is "NA". So why the atom name is "NA" instead of "NA+"?

In the updated "system.top" file, it is shown as
NA+ 948
CL- 1208

Because of this mismatch, the command below causes problems
$ gmx grompp -f minimization.mdp -r system_genion.gro -c system_genion.gro -p system.top -o system-min.tpr
Warning: atom name 70524 in system.top and system_genion.gro does not match (NA+ - NA)

What I do to work around is, change the "NA+" to "NA" in the "martini_v2.0_ions.itp" file.

But what is the standard way to deal with this issue?

Thank you!

Yours sincerely
Cheng

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1 week 3 days ago #8031 by Pim
Hi Cheng, yeah I know that happens, you can safely ignore the difference warnings in this case grompp - maxwarn 1or you can do what you did without problems. I personally prefer your solution, because on the end gromacs will take the names from the top file and NA is just a little more convenient to work with on the future than NA+ e.g. in selecting for visualization.

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