GROMACS version: 2018.8
GROMACS modification: No
Here post your question I am trying to run umbrella sampling via GROMACS 2018.8 version.
My system is of a ligand embedded in a lipid by layer membrane which i have prepared via CHARMM GUI.
Running the following command, i got error
Command line: gmx grompp -f step6.0_minimization.mdp -c step5_input.gro -p topol.top -o em.tpr
Setting the LD random seed to 2121802801
Generated 462 of the 465 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 326 of the 465 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘LIG’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘DOPC’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘DOPG’
turning H bonds into constraints…
Excluding 1 bonded neighbours molecule type ‘POT’
turning H bonds into constraints…
Excluding 1 bonded neighbours molecule type ‘CLA’
turning H bonds into constraints…
Excluding 2 bonded neighbours molecule type ‘TIP3’
turning H bonds into constraints…
ERROR 1 [file LIG.itp, line 13]:
** moleculetype LIG is redefined**
Please guide how to fix it.
i am uploading my “topol.top” file so you can review. topol.top (994 Bytes)
It seems you have #include “toppar/LIG.itp” twice in the file, as well as for every other .itp file. You only need them once, it’s not necessary to do so before setting up the posres files
There are few things that i need to ask. what is meant by this error
Fatal error: Distance between pull groups 1 and 2 (6.791968 nm) is larger than 0.49 times the box size (6.791871).
For pulling simulations i used pull1.mdp (2.0 KB) i have used pull_coord1_init = 0.00001 ; Initial distance set to 1.0 nm
pull_coord1_rate = 0.00005 ; 0.01 nm per ps = 10 nm per ns in pulling simulations because if i dont use them i get error Fatal error: Distance between pull groups 1 and 2 (6.791968 nm) is larger than 0.49 times the box size (6.791871).. now using these parameters i successfully did steered md simulations, prepared npt.tpr files for umbrella sampling. please find attached npt.mdp file npt_umbrella.mdp (2.0 KB). but when i run final umbrella sampling simulation using these parameters i get same error. md_umbrella.mdp (1.9 KB)
You need to make sure the pull groups you choose are never pulled to greater than 0.49 times the length of the box in the direction it’s pulling. So if you’re pulling in the z-direction, and the 2 pull groups are pulled up to 7 nm apart, your box should be at least 14 nm long in the z-direction
Instead of pull_coord1_geometry = distance use pull_coord1_geometry = direction and pull_coord1_vec = 0 0 1.
Use a larger water layer. Set Water thickness to 100 Å (or something).
I would recommend alternative 1.
By the way, why do you have pull_coord1_init = 0.00000001 and pull_coord1_rate = 0.00000005 in your umbrella simulation file? They can (or should) both be 0.
