Hi. My system contains 1 polymer and 1 drug molecule. After using the following command:
gmx_mpi grompp -f ions.mdp -c box.gro -p topol.top -o ions.tpr
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are: 2 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Number of degrees of freedom in T-Coupling group rest is 1053.00
NOTE 2 [file ions.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
As I said, my system consists of a polymer and a drug molecules. With this mdp file, when I simulated the polymer alone, there was no problem. But when I add the drug molecule, this error occurs.
The small non-zero charge is not really an issue, although I suggest to fix that and this must then be in the topology of the drug molecule. But you should never use a plain cut-off for Coulomb interactions.
I’ve raised this issue before, but users are in an impossible situation when running genion. If they specify a physically valid method like PME, they are warned that PME shouldn’t be used with a charged system. So to get around that, they switch to plan cutoff, at which point they get a warning that a plain cutoff simply shouldn’t be used. So, perhaps they resort to using -maxwarn to bypass things, which in my opinion, is a dangerous habit to adopt, because then it becomes normal to override important warnings to “make things work.”
Users need a way to tell grompp more explicitly that they are simply trying to add ions using the subsequent .tpr file, such that warnings related to physical validity are turned off. The .tpr file isn’t for a simulation, it’s just that we’re hacking the machinery to do something else - add ions.
Thanks Justin for your answer. I’m beginner in gromacs.
Now, what parameters should I change or delete and add in this mdp file to fix these two notes that the gromacs mentions? Please specify in detail.
Adding an integration option just for genion seems overkill. But since the error is emitted by grompp, somehow grompp needs to be told not to warn about the net charge.
For adding ions, it’s honestly irrelevant. You can use -maxwarn here if you want to get past the issues, just don’t make that a habit. And for anyone stumbling across this thread later, I only intend for that advice to be used here, until Berk comes up with a suitable workaround for the issue. Never use -maxwarn otherwise :)
upon executing gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr it shows error of net charge.
NOTE 2 [file topol.top, line 24632]:
System has non-zero total charge: 6.000000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Even though I used -maxwarn 2 flag, to get past the issue but it still shows the same error.
isn’t it weird when I try to replicate it, it shows error.
The -maxwarn flag has no impact on notes, and the appearance of a note should not cause grompp to fail (thus eliminating the need for -maxwarn in this context, because one no longer has to use plain cutoffs for Coulomb interactions).
Thanks for kind consideration.
It shows not only the “Notes” but also the error . Please have a look.
NOTE 2 [file topol.top, line 24632]:
System has non-zero total charge: 6.000000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
There were 2 notes
-------------------------------------------------------
Program: gmx grompp, version 2022.2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2172)
Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Then a separate ERROR message will be printed above in the terminal. Warnings can be bypassed with -maxwarn, notes are informative, but errors must be solved because they reflect a fatal problem.
You need to post what the actual error is. But this sounds like a very different topic from the original point of this thread, so to avoid confusion, please start a new discussion.
@jalemkul
Sorry for the confusion. It is the same error as the topic. Below is the error.
NOTE 2 [file topol.top, line 24632]:
System has non-zero total charge: 6.000000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Not finding a way to solve it. Just want to mention that I am replicating your tutorial and getting this error while executing
only change in the protocol what I did is, I chose the force field from the default gmx location (/usr/local/gromacs/share/gromacs/top/charmm36-mar2019.ff) rather downloading and extracting it in local directory.
A note and an error are different. The original topic regards notes and how to understand them. You show above a fatal error which says there is an error in your input file. This is not the same as the original topic and you need to provide the entire terminal output from grompp that contains the error. It will say ERROR not NOTE.