Gmx grompp -f minim.mdp -c DopGte.pdb -p topol.top -o dppc.tpr?

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1

Hello, anyone help me to solve this issue
gmx grompp -f minim.mdp -c DopGte.pdb -p topol.top -o dppc.tpr

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 1599052253

Generated 1114 of the 2701 non-bonded parameter combinations

Excluding 3 bonded neighbours molecule type ‘DOP’

Excluding 3 bonded neighbours molecule type ‘GTE’

WARNING 1 [file topol.top, line 23]:
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. Further information is available at
https://redmine.gromacs.org/issues/2884 , and a longer explanation of our
decision to remove physically incorrect algorithms can be found at
On The Importance of Accurate Algorithms for Reliable Molecular Dynamics Simulations | Theoretical and Computational Chemistry | ChemRxiv | Cambridge Open Engage .

ERROR 1 [file topol.top, line 23]:
Empty diagonal for a 3-dimensional periodic box

ERROR 2 [file topol.top, line 23]:
ERROR: The cut-off length is longer than half the shortest box vector or
longer than the smallest box diagonal element. Increase the box size or
decrease rlist.

There was 1 note

There was 1 warning

Program: gmx grompp, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1963)

Fatal error:
There were 2 errors in input file(s)

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

2

What is the size of the periodic box? How have you generated the periodic box of the system? Have you solvated the system?

3

No sir I didn’t solvate the system. I just used the ATB generated.itp files and and my input. Using the gmx grompp -f minim.mdp -c input.pdb …

4

I’d recommend using gmx editconf to generate a simulation box for your system and gmx solvate to solvate it. If you want a basic box you can use gmx solvate directly. I would also recommend reading Getting started - GROMACS 2024.2 documentation and doing some of the tutorials at https://tutorials.gromacs.org/ and/or GROMACS Tutorials.

5

Can u please tell me how to use ?

6

I’m afraid I can’t give detailed instructions right now. If you do the first tutorial on https://tutorials.gromacs.org I think you will go through the most important steps.

7

Hello sir , I use gmx editconf commands… .gro files is generated after that using the commands line
gmx grompp… Same errors occurs

8

Same error?

If you’ve generated a box with sufficient margin I’d at least expect another error.

9

yes no difference in error. same error use gmx edi… after use gmx grompp

10

what is your full gmx editconf command?

also as suggested above, please do the tutorials first.

11

gmx editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -box 6.41840 6.44350 6.59650 this is the commands i follow . the box are created but after I did not do the step gmx grompp -f minim.mdp -c dppc128.pdb -p topol_dppc.top -o dppc.tpr? also I assign the water than go direct for ions addition ?

12

try gmx editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -d 1

13

Okay after using this commands they will automatically assigned box size for it ? Or after this step I will again do for box

14

please do the tutorials,https://tutorials.gromacs.org/

15

The skeleton of tutorial is different. That’s why asked from expert. New user and also in the tutorial they gmx pdb2gmx… Start from protein so I am dealing with protein that’s why trouble in creating of topology