Ewald with net charge for large capsid

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1

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Hello,

I have been trying to run an MD on 60-mer capsids. I have tried 3 different force fields and am unsure if I am doing this correctly. I am still learning the commands. This one currently I am using Amber03. It gives me this warning about the ewald in a system of net charge. What I was doing was trying to go by the tutorial and I did use the maxwarn and then created the ions.tpr. Then tried to gmx genion -s ions.tpr -o xxx -p xxx neutral, Group 13-sol…
I am unsure if I am doing this right. And how I should manipulate the ions.mdp file to correct my problem. Can someone please explain to me how to correct this, if I am doing the commands incorrectly or if I need to make adjustments in the mdp and how to properly do so.

Thanks,
Heather
GROMACS: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /mnt/c/users/haten/onedrive/desktop/gromacs
Command line:
gmx grompp -f ions.mdp -c solvate.gro -p topol.top -o ions.tpr

Ignoring obsolete mdp entry ‘ns_type’
Setting the LD random seed to -1119564007
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_A1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_B1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_C1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_D1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_E1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_F1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_G1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_H1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_I1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_J1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_K1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_L1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_M1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_N1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_O1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_P1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_Q1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_R1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_S1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_T1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_U1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_V1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_W1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_X1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_Y1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_Z1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_a’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_b’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_c’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_d’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_e’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_f’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_g’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_h’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_i’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_j’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_k’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_l’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_m’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_n’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_o’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_p’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_q’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_r’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_s’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_t’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_u’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_v’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_w’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_x’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_y’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_z’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_1’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_2’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_3’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_4’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_5’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_6’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_7’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_8’
Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 1 [file topol.top, line 164]:
System has non-zero total charge: -175.000000
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.

WARNING 1 [file topol.top, line 164]:
You are using Ewald electrostatics in a system with net charge. This can
lead to severe artifacts, such as ions moving into regions with low
dielectric, due to the uniform background charge. We suggest to
neutralize your system with counter ions, possibly in combination with a
physiological salt concentration.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net
Charge
J. Chem. Theory Comput. 10 (2014) pp. 381-393
-------- -------- — Thank You — -------- --------

Analysing residue names:
There are: 33280 Protein residues
There are: 946537 Water residues
Analysing Protein…
Number of degrees of freedom in T-Coupling group rest is 7209369.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 280x280x280, spacing 0.115 0.115 0.115
Estimate for the relative computational load of the PME mesh part: 0.18
This run will generate roughly 256 Mb of data

There was 1 note

There was 1 warning

Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2353)

Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

2

Hi,
if you are generating a tpr file to have an input file for gmx genion, then you can ignore this warning increasing the level of max warning allowed to 1 in grompp (only for this step), or you can change the setting in mdp file (e.i use an empty mdp) (but also only for this step), like is described here Molecular dynamics simulation of a small protein using GROMACS — GROMACS tutorials https://tutorials.gromacs.org documentation

I hope it helps
Alessandra

3

Hello,
yes thank you this added the NA and CL. Thank you!!

I have one more questions for you. I minimized the system and now I need to do the NPT, however in the tutorial it shows the two equilibration states of NVT (temp) and NPT (pressure,density) My advisor said I should only be doing NPT. However, my question is do I need the NVT temperature also? or can I just run the gmx grompp -f npt.mdp -c em.gro -r em.gro -p topo.top -o npt and the mdrun still work?, because it keeps failing due to the lincs when I only run the npt. I have changed the constraints to all-atoms, as this is what I have read in previous capsid MD studies. I am unsure if I am correctly editing it in the file. If I should address this question seperately please let me know.

thanks,
Heather

4

I usually suggest first equilibrating temperature under NVT, then pressure with NPT. At the outset of the run, velocities are random, so this can cause wild pressure oscillations that lead to instability in the barostat. There is no “one size fits all” protocol for equilibration, and sometimes going right to NPT is fine. But if it’s crashing, clearly there’s an issue (may be something else entirely, but there’s nothing “wrong” with equilibrating under an NVT ensemble, followed by NPT - the point of equilibration is to reach a stable state for production simulations under the ensemble you want).

5

ok, thank you Justin.