At first you should compile GROMACS-CP2K.
https://manual.gromacs.org/current/install-guide/index.html#building-with-cp2k-qm-mm-support
If you dont know what to do that, please ask someone around who has experience in building programs from source files. As it requires access to you machine to help.
Second, you are using wrong tutorial, correct one is
https://github.com/bioexcel/gromacs-2022-cp2k-tutorial
Okay sir
Thankyou so much.
Dear Dmitry,
I successfully run TD-DFT calculation with gmx_cp2k interface. I got spec.xvg. Also, I would like to have HOMO-LUMO (ground and excited) state electron density image from TD-DFT.
Previously, you have suggested me for using the below keyword for homo-lumo in the section to &FORCE_EVAL / &DFT:-
&PRINT
&MO_CUBES
NHOMO 1
NLUMO 1
&END MO_CUBES
&END PRINT
Now, my query is where I can insert these keywords in .inp file for TD-DFT HOMO-LUMO?
With regards,
Ranabir
Hello sir
I’m following the tutorial link which you shared,
Go to nma directory:
cd nma
this is the first step of it, I wrote cd nma but error showed that there is no nma directory. I cretaed a directory by naming it as nma and then i moved on to the second step “gmx pdb2gmx -f nma.pdb” if i write this code I should get the forcefild and water model to choose but i’m not getting it…
can you please help me out …
You did not downloaded tutorial
I’m following this tutorial link sir…
@Pallavi,
Kindly learn first how to use Linux os. Then try to install and run gromacs properly. Gromacs-CP2k QMMM simulation is a very advanced stage. So please 1st learn the basics.
Dear Dmitry,
I am happy to inform you that I successfully run gromacs_CP2k QM/MM in my institute’s supercomputer.
Now, I am facing some doubts about setting up QM/MM files.
First, I have minimized and equilibrated (MM-NVT, MM-NPT) my QM/MM system (DNA-Ligand in water) then I have performed QM-MM-EM, QM-MM-NVT as per your tutorial. Is QM-MM-NPT not needed before the final QM/MM production run?
Also, it will be very helpful if you could provide me with the necessary mdp files to set up QM/MM simulation.
With regards,
Ranabir
Hi Ranabir,
NPT is possible, but strictly saying you will not get better results with pressure coupling in QMMM.
For the QMMM I would suggest to use just NVT.
Best,
Dmitry
Thanks, Dmitry for your kind suggestion.
Dear Dmitry,
I have run a 300ns classical MD simulation of a DNA-Ligand system in water. Now, I would like to run the system’s QM/MM (TDDFT) simulation. I have taken the last frame from the 300ns MD simulation.
My query is how many steps (minimum) do I have to perform for QM/MM simulation (EM, NVT & Production run)?
With regards,
Ranabir
For ground state typically 1-10 ps equilibrations should be enough
Dear Dmitry,
Thanks for your kind reply.
1 ps means nsteps=1000 where dt=0.001.
My system consists of 173 atoms. I am using our institute HPC system with 120 cores (Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz). But it is taking 6-8 hrs. to complete each step.
Kindly advise me on how can I proceed with such a biosystem to run TDDFT calculation.
Thanking you,
Ranabir
I mean first you should relax your system with ground state DFT for 1 ps.
I really could not help you here, sorry. It is too dependent on combination of your hardware setup, functional, cut-offs, etc. But 173 atoms is really big for TDDFT dynamics, I would not recommend to use more than 50 atoms for such calculations in dynamics.
Dear Dmitry,
For any biological system, 50 atoms are very less. Even a drug/ligand consists of more than 50 atoms.
Anyway, could you give me some suggestions to run TDDFT?
With regards,
Ranabir
Hi Ranabir,
Unfortunately, I did not tried yet myself TDDFT dynamics with CP2K (efficient gradients was appeared for that only with CP2K v9.1). I have a plans to look into that but could not give you any hints now.
Best,
Dmitry
Hi Dmitry,
Thank you.
Kindly update me if you get anything.
With regards,
Ranabir
Hello sir
Sir, I have downloaded the tutorial of GROMACS-2022/CP2K QMMM interface. Initaially it went well but now i have stuck in the 5th step where I have to run this command
sbatch run-em.sh
I’m getting errors here
sbatch: error: resolve_ctls_from_dns_srv: res_nsearch error: Unknown host
sbatch: error: fetch_config: DNS SRV lookup failed
sbatch: error: _establish_config_source: failed to fetch config
sbatch: fatal: Could not establish a configuration source
and when i checked the status of slurmctld…
$ sudo service slurmctld status
× slurmctld.service - Slurm controller daemon
Loaded: loaded (/lib/systemd/system/slurmctld.service; enabled; vendor preset: enabled)
Active: failed (Result: exit-code) since Thu 2022-08-04 11:31:24 IST; 3h 38min ago
Condition: start condition failed at Thu 2022-08-04 15:09:16 IST; 8s ago
└─ ConditionPathExists=/etc/slurm/slurm.conf was not met
Docs: man:slurmctld(8)
Main PID: 1635540 (code=exited, status=1/FAILURE)
CPU: 36ms
Aug 04 11:31:24 GROMACS systemd[1]: Started Slurm controller daemon.
Aug 04 11:31:24 GROMACS systemd[1]: slurmctld.service: Main process exited, code=exited, status=1/FAILURE
Aug 04 11:31:24 GROMACS systemd[1]: slurmctld.service: Failed with result ‘exit-code’.
Aug 04 14:40:26 GROMACS systemd[1]: Condition check resulted in Slurm controller daemon being skipped.
Aug 04 14:40:59 GROMACS systemd[1]: Condition check resulted in Slurm controller daemon being skipped.
Aug 04 14:41:08 GROMACS systemd[1]: Condition check resulted in Slurm controller daemon being skipped.
Aug 04 14:46:26 GROMACS systemd[1]: Condition check resulted in Slurm controller daemon being skipped.
Aug 04 14:56:32 GROMACS systemd[1]: Condition check resulted in Slurm controller daemon being skipped.
Aug 04 15:09:16 GROMACS systemd[1]: Condition check resulted in Slurm controller daemon being skipped.
please do help me with this sir.
Thank you in advance.
Hi run-em.sh script is dependent on an actual configuration of your cluster. You might need to modify it. Ask administrators how to run it correctly, probably it should be the same way as you running normal GROMACS.
Okay sir.
Thank you
