Gpu update giving error with protein ligand complex

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1

GROMACS version: 2022.3
GROMACS modification: No
Here post your question:

I am doing a simulation of a membrane protein complex with a small molecule ligand. I am running it on a cluster with nodes having four GPUs. I have seen that uisng all four GPUs and enabling direct GPU communication makes my simulation significantly faster when I tried with just the protein (without the ligand). The simualtion files are generated using CHARMM-GUI.

However, when I try to run the simulation with the system conatining ligand, I get the following error.

“Inconsistency in user input:
Update task on the GPU was required,
but the following condition(s) were not satisfied:
Domain decomposition is only supported with constraints when update groups are
used. This means constraining all bonds is not supported, except for small
molecules, and box sizes close to half the pair-list cutoff are not supported.”

My md.log file says “When checking whether update groups are usable:
At least one moleculetype does not conform to the requirements for using update groups”

My mdp files is the following:
integrator = md
dt = 0.002
nsteps = 500000000
nstxout = 50000
nstvout = 50000
nstfout = 50000
nstcalcenergy = 100
nstenergy = 1000
nstlog = 1000
;
cutoff-scheme = Verlet
nstlist = 100
rlist = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
coulombtype = PME
rcoulomb = 1.2
;
tcoupl = V-rescale
tc_grps = SOLU MEMB SOLV
tau_t = 1.0 1.0 1.0
ref_t = 303.15 303.15 303.15
;
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
;
nstcomm = 100
comm_mode = linear
comm_grps = SOLU_MEMB SOLV

And the commands I am using to run the simulation is
gmx grompp -f step7_production.mdp -o md.tpr -c step6.6_equilibration.gro -p topol.top -n index.ndx
gmx mdrun -v -deffnm md -ntomp 13 -ntmpi 4 -nb gpu -bonded gpu -update gpu -pme gpu -npme 1 -ntomp_pme 5

Any help on how to solve this issue will be appreciated.

Thank you

2

My guess is that your ligand has all hydrogens at the end instead of following after the heavy atom they are connected to. This prevents the use of update groups.

From version 2023 onward, the reason why update groups can’t be used is written in the log file.

3

Thank you for your reply.

I just checked the input .gro file and the hydrogens are all at the end as you pointed out. Is there any way I could circumvent this problem?

Also, just curious, why exactly does order of atoms in the input file affect the “update groups” feature?

Thank you

4

You could manually reorder the lines in the .gro file and reorder the topology, but that’s tedious.

Theoretically there is no reason why update groups couldn’t work, but is quite some effort to reorder atoms in the input to get the atoms in update groups to be consecutive.

1 Like
5

I manuall reordered them in my initial input file to CHARMM-GUI. So, all the inputs to GROMACS were in the right order and I was able to get it to work.
Thanks for your help and suggestions.