I am performing coarse grain simulation of peptides packed in a box but after addition of the solvent the box size is changing. The initial box size is set to up in this command: gmx editconf -f Protein_A-CG.pdb -o Protein_A-CG.gro -box 76.196 76.196 76.196 -angles 90 90 90. The final is around 12.33846 12.74318 12.62067. Can you help me how to fix this?
@Kapali: Please submit such questions to “User discussions” in the future. Your post is not related to third party tools, so I moved it to the correct category.
Could you explain more in detail what your problem is? I don’t understand.
Does the box change when you do gmx solvate? That sounds very strange. Or does it change during simulation? That is what you would expect if you are running with pressure coupling (in an NPT ensemble). If you don’t want that then don’t use pressure coupling.
I’ve been working on simulating a system of peptides, preparing both an atomistic and coarse-grained (CG) system using Packmol. I expected the box size for the coarse-grained simulation to be smaller since multiple atoms are represented as single “beads” in the CG system, reducing the total number of particles. However, I encountered the opposite: the box size in the coarse-grained system is larger than the atomistic one. So I have done various things given below.
- gmx_mpi editconf -f Protein_A-CG.pdb -o Protein_A-CG.gro -d 1.0 -c -bt orthorhombic; this command is not working for orthorhombic system (although I want orthorhombic only) then I used this command:gmx_mpi editconf -f Protein_A-CG.pdb -o Protein_A-CG.gro -d 1.0 -c -bt triclinic. I used this because somehere I read GROMACS does not have a direct
orthorhombicoption for box type. But the box size that is coming is :
No velocities found
system size : 11.436 11.876 11.743 (nm)
center : 5.733 6.122 6.012 (nm)
box vectors : 0.000 0.000 0.000 (nm)
box angles : 0.00 0.00 0.00 (degrees)
box volume : 0.00 (nm^3)
shift : 0.985 0.816 0.859 (nm)
new center : 6.718 6.938 6.871 (nm)
new box vectors : 13.436 13.876 13.743 (nm)
new box angles : 90.00 90.00 90.00 (degrees)
new box volume :2562.12 (nm^3)
For the same system in atomistic box size is coming 76.196 76.196 76.196.
- I adjusted it using the command: /opt/gromacs-2023.2/bin/gmx_mpi editconf -f Protein_A.pdb -o Protein_A.gro -box 76.196 76.196 76.196 -angles 90 90 90 (orthorhombic system), but I am getting this error:
Fatal error:
Too many LINCS warnings (1001)
If you know what you are doing you can adjust the lincs warning threshold in
your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
Can you help me with few things, why the box size is coming bigger in case of coarse grain? How should I run it for orthorhombic system and if I should use second method, how should I resolve the error.
As you see from the output angles, the default output of a generated triclinic box is orthorhombic.
You say that the box dimensions are 76.196 nm for the atomistic system. That is huge. Or do you mean 7.617 nm?
Do you really expect the box sizes to be identical? From where did you get the 7.617 nm (assuming it is the correct number) box size of the atomistic system? How was the Protein_A-CG.pdb generated? It is difficult for us to explain discrepancies between two systems unless we know how they were created.