CHARMM README Script towards successful Gromacs Minimization Inquiry

User discussions
1

GROMACS version: 2022.1
GROMACS modification:No
Here post your question:

Hello,

for the above topic I can not seem to complete the final starting step of CHARMM Step 6.0 minimization of my protein-membrane implant. A successfully visualized step5_assembly.pdb was generated inidicating Steps 1-5 success, the CHARMM generated Gromacs file contained the below files:

toppar
topol.top
step7_production.mdp
step6.6_equilibration.mdp
step6.5_equilibration.mdp
step6.4_equilibration.mdp
step6.2_equilibration.mdp
step6.3_equilibration.mdp
step6.0_minimization.mdp
step6.1_equilibration.mdp
step5_input.psf
step5_input.gro
step5_input.pdb
README
index.ndx

and the README Script was successfully generated within the generated Gromacs file exhibiting:

For MPI parallelizing, we recommand following command:
mpirun -np $NUM_CPU gmx mdrun -ntomp 1

set init = step5_input
set rest_prefix = step5_input
set mini_prefix = step6.0_minimization
set equi_prefix = step6.%d_equilibration
set prod_prefix = step7_production
set prod_step = step7

I navigated to my Gromacs Working Directory containing the above files and within my iTerm pasted the Minimization Command within the Gromacs Folder:

gmx grompp -f {mini_prefix}.mdp -o {mini_prefix}.tpr -c {init}.gro -r {rest_prefix}.gro -p topol.top -n index.ndx
gmx_d mdrun -v -deffnm ${mini_prefix}

alone as well as in combination with the just the parallelization command as well as with its associated lines and all of these combinations resulted in the below several errors:

Error in user input:
Invalid command-line options
In command-line option -f
File ‘.mdp’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -c
File ‘.gro’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -r
File ‘.gro’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)

My understanding is that I am supposed to just input one of the combinations that I did; please let me know what exact commands I would need to input to successfully generate my model minimization? (I could not discovery anywhere a direct tutorial on this topic.). Thanks if you can help:)

2

The README file is a shell script. Run it. Don’t pick and choose lines to try to execute. If you have issues with files provided by CHARMM-GUI, it is probably better to ask help from them as these are not really GROMACS problems per se.

3

Hello Justin thank you for your kind update:).

Unfortunately CHARMM does not have a detailed tutorial towards this inquiry nor did they answer the same inquiry. I am not sure what you men by `Run it´ above, if you can be more detailed great if this is not the forum for this any longer understandable, thanks:)

4 
chmod +x README
./REAMDE

Rename it if you like to make more sense, but that’s it.

5

Hi Justin thanks a bunch for the command which is now executing.

The executed command ran through the minimization, however, precipitated an error towards the first step of the equilibration i.e. the step6.1_equilibration.gro was not generated, probably because of the previous below fatal error:

Fatal error:
6 particles communicated to PME rank 4 are more than 2/3 times the cut-off out
of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.

I could not find a topic on this error on this forum nor the CHARMM Forum, if this inquiry is beyond the scope of this forum (i.e. maybe a CHARMM Inquiry) understandable, if not and it is a -maxwarn 1 and or if their is another solution feel free to respond, thanks:)

6

You have a generic failure message; you can search this forum and find thousands of posts with that error and how to solve it, including specific troubleshooting advice on the GROMACS website (it’s an FAQ).

7

Hi Justin thank you for your kind update I will relook (I pasted the whole error in maybe thats why I could not find it), Best, Joel :)

8

Hi Justin I seem to have the README CHARMM/Gromacs protein-membrane system now equilibrating (on the Final Stage 6.6 step6.6_equilibration.inp from the README File), however,
have bad practiced Maxwarned the below WARNINGS and NOTE, would you recommend that I
research this topic more deeply towards changing this thermostat/barostat etc. or may I maxwarn these if I am simply generating this protein-membrane system to compare it against the existing OPM already generated protein-membrane system?

WARNING 1 [file step6.6_equilibration.mdp]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution, and should not be used for new production simulations (in
our opinion). We would recommend the V-rescale thermostat.

WARNING 2 [file step6.6_equilibration.mdp]:
The Berendsen barostat does not generate any strictly correct ensemble,
and should not be used for new production simulations (in our opinion).
For isotropic scaling we would recommend the C-rescale barostat that also
ensures fast relaxation without oscillations, and for anisotropic scaling
you likely want to use the Parrinello-Rahman barostat.

NOTE 1 [file step6.6_equilibration.mdp]:
Removing center of mass motion in the presence of position restraints
might cause artifacts. When you are using position restraints to
equilibrate a macro-molecule, the artifacts are usually negligible.

Thanks:), Joel 🚀

9

The warnings tell you how to adjust the input files to be more robust. The note implies you should probably be using refcoord-scaling though likely it won’t matter much.

10

Hi Justin thank you for your kind update:).

I will change this for enrichment 🚀

11

Hi Justin,

I reached the Final Step of the CHARMM/Gromacs protein-membrane simulation:
step7_production.mdp from the README File. After execution of this final command
from the README File I encountered a host of Notes, LINCS Warnings, Warning, IMPORTANT notice, and a Fatal Error that wouldnt allow the simulation to continue via the non-generation of the .gro, tpr, topol files.

My question is should I just use the Membrane-Protein OPM Coordinate File in this case since maybe this is something particular to my protein (similar to when you recommended I use CHARMM for my transmembrane protein that would not Gromacs membrane implant)?

Below are the host of problems:

NOTE 1 [file step7_production.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

NOTE 2 [file topol.top, line 42]:
The bond in molecule-type POPC between atoms 31 C21 and 32 O22 has an
estimated oscillational period of 2.1e-02 ps, which is less than 10 times
the time step of 4.0e-03 ps.
Maybe you forgot to change the constraints mdp option.

Step 2446, time 9.784 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000026, max 0.000202 (between atoms 82026 and 82028)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 30.0 0.1111 0.1111 0.1111

Step 2450, time 9.8 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000024, max 0.000369 (between atoms 84260 and 84261)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 30.3 0.1111 0.1111 0.1111

Step 2453, time 9.812 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000025, max 0.000266 (between atoms 84260 and 84261)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 30.6 0.1111 0.1111 0.1111

Step 2455, time 9.82 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000024, max 0.000363 (between atoms 47073 and 47076)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 34.6 0.1111 0.1111 0.1111

Step 2469, time 9.876 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000025, max 0.000299 (between atoms 47073 and 47076)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 36.0 0.1111 0.1111 0.1111

Step 2474, time 9.896 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000025, max 0.000236 (between atoms 104929 and 104931)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 31.2 0.1111 0.1111 0.1111

Step 2491, time 9.964 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000026, max 0.000283 (between atoms 45436 and 45437)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 32.0 0.1111 0.1111 0.1111
step 2500, will finish Thu Nov 3 23:30:01 2022
Step 2570, time 10.28 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000024, max 0.000289 (between atoms 64022 and 64023)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 30.3 0.1111 0.1111 0.1111
step 2600, will finish Thu Nov 3 23:29:55 2022
Step 2602, time 10.408 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000023, max 0.000315 (between atoms 69564 and 69565)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 30.4 0.1111 0.1111 0.1111

Step 2621, time 10.484 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000023, max 0.000323 (between atoms 91275 and 91278)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 38.3 0.1111 0.1111 0.1111

Step 2624, time 10.496 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000022, max 0.000274 (between atoms 91275 and 91277)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 35.5 0.1111 0.1111 0.1111

Step 2626, time 10.504 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000023, max 0.000223 (between atoms 81103 and 81104)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 37.0 0.1111 0.1111 0.1111

Step 2631, time 10.524 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000027, max 0.000895 (between atoms 93450 and 93451)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 31.8 0.1111 0.1111 0.1111

Step 2633, time 10.532 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000023, max 0.000338 (between atoms 111309 and 111310)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 35.6 0.1111 0.1111 0.1111

Step 2636, time 10.544 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000023, max 0.000433 (between atoms 93450 and 93451)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 36.0 0.1111 0.1111 0.1111

Step 2638, time 10.552 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000023, max 0.000225 (between atoms 86317 and 86318)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 33.1 0.1111 0.1111 0.1111

Step 2643, time 10.572 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000024, max 0.000743 (between atoms 93450 and 93451)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 38.3 0.1111 0.1111 0.1111

Step 2645, time 10.58 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000022, max 0.000232 (between atoms 112829 and 112831)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 36.3 0.1111 0.1111 0.1111

Step 2648, time 10.592 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000021, max 0.000219 (between atoms 93450 and 93451)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 31.8 0.1111 0.1111 0.1111

Step 2650, time 10.6 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000027, max 0.000917 (between atoms 93450 and 93451)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 32.5 0.1111 0.1111 0.1111

Step 2655, time 10.62 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000032, max 0.001419 (between atoms 93450 and 93452)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 32.3 0.1111 0.1111 0.1111

Step 2660, time 10.64 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000023, max 0.000281 (between atoms 94593 and 94594)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 31.1 0.1111 0.1111 0.1111

Step 2667, time 10.668 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000023, max 0.000555 (between atoms 93450 and 93451)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 37.9 0.1111 0.1111 0.1111

Step 2669, time 10.676 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000023, max 0.000291 (between atoms 111309 and 111310)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 33.7 0.1111 0.1111 0.1111

Step 2672, time 10.688 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000023, max 0.000344 (between atoms 111309 and 111310)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 31.2 0.1111 0.1111 0.1111

Step 2674, time 10.696 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000027, max 0.000864 (between atoms 93450 and 93451)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 32.8 0.1111 0.1111 0.1111

Step 2686, time 10.744 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000024, max 0.000581 (between atoms 93450 and 93451)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 31.4 0.1111 0.1111 0.1111

Step 2687, time 10.748 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000024, max 0.000278 (between atoms 101546 and 101547)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 42.1 0.1111 0.1111 0.1111

Step 2690, time 10.76 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000024, max 0.000265 (between atoms 101546 and 101548)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 38.1 0.1111 0.1111 0.1111

Step 2692, time 10.768 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000027, max 0.000743 (between atoms 93450 and 93452)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 32.1 0.1111 0.1111 0.1111
step 2700, will finish Thu Nov 3 23:30:18 2022
Step 2701, time 10.804 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000026, max 0.000315 (between atoms 81088 and 81090)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 31.0 0.1111 0.1111 0.1111

Step 2704, time 10.816 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000025, max 0.000290 (between atoms 61263 and 61264)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 37.5 0.1111 0.1111 0.1111

Step 2705, time 10.82 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001571, max 0.131338 (between atoms 93442 and 93443)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 90.0 0.1111 0.1257 0.1111

Step 2706, time 10.824 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.014135, max 1.146123 (between atoms 93442 and 93443)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 90.0 0.1257 0.2384 0.1111
93439 93441 90.0 0.1111 0.1430 0.1111
Wrote pdb files with previous and current coordinates

Step 2707, time 10.828 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.189662, max 15.854660 (between atoms 93442 and 93443)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 90.0 0.2384 1.8726 0.1111
93439 93440 74.1 0.1116 0.1115 0.1111
93439 93441 36.5 0.1430 0.1100 0.1111
Wrote pdb files with previous and current coordinates

Step 2708, time 10.832 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.028915, max 2.061976 (between atoms 93439 and 93440)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 90.0 1.8726 0.2512 0.1111
93439 93440 90.0 0.1115 0.3402 0.1111
93439 93441 30.1 0.1100 0.1074 0.1111
93450 93451 51.9 0.1111 0.1111 0.1111
93450 93452 32.5 0.1111 0.1109 0.1111
Wrote pdb files with previous and current coordinates

Step 2709, time 10.836 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.420224, max 31.248405 (between atoms 93442 and 93443)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
93442 93443 90.0 0.2512 3.5828 0.1111
93439 93440 90.0 0.3402 0.1206 0.1111
98062 98063 90.0 0.1111 0.7434 0.1111
98062 98064 90.0 0.1111 1.7781 0.1111

step 2709: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 93443 and 93445
at distance 3.560 which is larger than the table limit 2.323 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

Fatal error:
4 particles communicated to PME rank 6 are more than 2/3 times the cut-off out
of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.

If this is something I can repair feel free to recommend me to trouble-shoot these errors in lieu of using just the OPM Protein-Membrane Coordinate File, thanks:) Joel 🚀

12

I made that recommendation because using InflateGRO is far too clunky to deal with a complicated case; I don’t know anything about the suitability of your particular protein coordinate file.

You have one problem, which is shown with the LINCS warnings. Probably there is a bad clash somewhere that can’t be resolved. Maybe that’s within the protein itself (look in the vicinity of the quoted atom numbers). There’s not much to go on here or suggest beyond what is repeatedly stated on this forum for investigating such issues. With a complex system like you’re dealing with, you may need to simplify, minimize the protein alone before embedding, etc.

13

Hi Justin thank you for your kind update:).

Is it standard to just use the OPM Protein-Membrane Coordinate File in lieu of trouble shooting this system in this case? (My goal was to generate this protein-membrane system and compare the membrane positions with the OPM Systems and then select the best fit system although as up to now both systems seem to be the same.). Thanks:)

14

I honestly have no idea.

15

Hi Justin thank you again for your kind update:).

I may just minimize this regardless for enrichment, thanks:)🚀