GROMACS version: 2020.1-1
GROMACS modification: No
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Dear experts.
I’m following a GROMACS tutorial. Thanks to the kind guide, I followed all steps without a problem…until I encounter the problem which haunted me for 4 days.
During the second tutorial (Membrane Protein), I cannot generate a .tpr file using gromp (gmx grompp -f minim.mdp -c dppc128.pdb -p topol_dppc.top -o dppc.tpr) (KALP-15 in DPPC).
===massage start===
Ignoring obsolete mdp entry ‘ns_type’
NOTE 1 [file minim.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to -1621490062
WARNING 1 [file ffnonbonded.itp, line 3123]:
Bondtype LJ-14 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
old: 0.00261735 2.63413e-06 0.00261735 2.63413e-06
new: OW OW 1 3.31400e-04 3.36000e-07
Generated 813 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type ‘DPPC’
Excluding 2 bonded neighbours molecule type ‘SOL’
WARNING 2 [file topol_dppc.top, line 26]:
The GROMOS force fields have been parametrized with a physically
incorrect multiple-time-stepping scheme for a twin-range cut-off. When
used with a single-range cut-off (or a correct Trotter
multiple-time-stepping scheme), physical properties, such as the density,
might differ from the intended values. Since there are researchers
actively working on validating GROMOS with modern integrators we have not
yet removed the GROMOS force fields, but you should be aware of these
issues and check if molecules in your system are affected before
proceeding.
Analysing residue names:
There are: 128 Other residues
There are: 3655 Water 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 41127.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 56x56x56, spacing 0.115 0.115 0.118
Estimate for the relative computational load of the PME mesh part: 0.18
This run will generate roughly 2 Mb of data
There was 1 note
There were 2 warnings
Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2353)
Fatal error:
Too many warnings (2).
If you are sure all warnings are harmless, use the -maxwarn option.
===massage end===
and dppc.tpr not generated.
And this seems inevitable to me because when copy from [pairtypes] lipid.itp to [pairtypes] ffnonbonded.itp, there are two identical contents which will cause crush each other.
[pairtypes] ffnonbonded.itp has ‘OW OW 1 3.31400e-04 3.36000e-07’
[pairtypes] lipid.itp has ‘OW OW 1 0.0026173456 2.634129e-06’
I cannot find a solution for this problem from guide. Guide indicate to delete or replace HW in .itp but not OW.
Should I delete one of them?
Actually, I already deleted “[pairtypes] ffnonbonded.itp has ‘OW OW 1 3.31400e-04 3.36000e-07’” but later, I also encountered failure (Reading structure file Select group to position restrain Segmentation fault) when I preceed to pack the lipids around the protein
It seem that every GROMAS novices can solve this problem easily. But I can’t do. I retried this part for 6 times and same warnings are reappeared.
I sincerely thanks for your attention and please help me if you could spare some times.
(ps: In case of a second messege, I figured out this warning caused by using old algorithm and could be solved by using -maxwarn 1 command.
reference: molecular dynamics - Error in GROMACS for adding ions to a solution - Matter Modeling Stack Exchange)