Hi!

Not sure, but the definition of gmx genion is that the command 'randomly replaces solvent molecules with monoatomic ions'.

I guess the error you get is linked to the fact that you have no solvent (no water, i.e. no SOL molecules) in your system and therefore in your topology file, so when the command tries to exchange solvent molecules with ions it obviously fails since there are no molecules to replace.

Is you system solvated?

Hi Pankaj, since your error refers to top-file and it says that the molecule was not found in molecules it means that you need to add there. The routine genion is replacing the solvent molecules.

Check mailing list archive: https://gromacs.org-gmx-users.maillist.sys.kth.narkive.com/6SRHzI65/genion-doesn-t-recognize-sol-in-top-file

HI,

I think you did forget some previous steps like ( Step Three: Defining the Unit Cell & Adding Solvent ) please check the bottom of the topol.top file ( status of #ifdef and / or #include statements ) or molecule type

then perform adding ions,which gives appropriate extra charge information.

Please check this link for further information

https://www.mail-archive.com/[email protected]/msg41751.html

https://mini.ourphysics.org/wiki/index.php/Tricks_in_Gromacs#:~:text=genion%20doesn't%20recognize%20SOL%20in%20top%20file&text=Each%20type%20of%20molecule%20in%20your%20%5B%20molecules%20%5D%20section%20of%20your%20.&text=top%20file%20doesn't%20have,to%20refer%20to%20them%20later.

https://gromacs.org-gmx-users.maillist.sys.kth.narkive.com/6SRHzI65/genion-doesn-t-recognize-sol-in-top-file

Hi

Please Check the last line of topol.top file and it should contain SOL the molecule type in it.

HI Nicola Piasentin Thanks for the response I have checked the totpol.top file in which sol is present after running the command. What do you mean by solvated system?

Thanks for your response and suggestions Sushma .P Satyaranjan Biswal Asdrubal Lozada Inna Ermilova Nicola Piasentin

Hi Pankaj Bhatt , I mean if you have solvent molecules in your system, but if SOL is present in the topology then you are fine.

Then I would follow the approach of the other answers you got here: first run your topology under the dos2unix command just to check if GROMACS is stopping because of weird non-Unix characters, and if this doesn't work then just run

gmx genion -s ions.tpr -o solv_ions.gro -pname NA -nname CL -neutral

and manually update your topology by adding after SOL the numbers of CL and NA that genion inserted and #including their .itps from ff's directory.

Nicola Piasentin Thanks for suggestion. i have run the command gmx genion -s ions.tpr -o solv_ions.gro -pname NA -nname CL -neutral it is running but in topol.top file no CL added when I check.....

Can you help more

I have attached the file please check. Looking for your more suggestions.

When I am adding CL manually than proceeding with

gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr

Than i am also receiving error

Fatal error:

number of coordinates in coordinate file (solv_ions.gro, 62615)

does not match topology (topol.top, 62630)

Thanks for your help.

Pankaj Bhatt yes, the error is right since you still haven't added the ions.

From the .docx file I see that gmx genion added 5 CL molecules (the residues 19424 to 19428 at the end of your .gro file). Since you run the command

gmx genion -s ions.tpr -o solv_ions.gro -pname NA -nname CL -neutral

and not

gmx genion -s ions.tpr -o solv_ions.gro -pname NA -nname CL -neutral -p topol.top

that is, you didn't give the topology to genion, the .top file has not been updated. You manually updated the topology as we suggested but only partially: this line is correct

#include "./charmm36-mar2019.ff/ions.itp"

but you still have to say that there are ions present in the system, in particular five of them. Here (end of topology)

[ molecules ]

; Compound #mols

Protein 1

LIG 1

SOL 19001

is where GROMACS looks for when it checks WHAT is present in your system. The line added by you just tells WHERE to find the parameters to use!

These last lines then have to be modified keeping in mind that genion removed 5 water molecules and added 5 CL ions, that is

[ molecules ]

; Compound #mols

Protein 1

LIG 1

SOL 18996 # taken away 5

CL 5 # 5 new added

I tried to explain everything, let me know if you are still getting an error. Hope this helps :D

Thanks Nicola Piasentin I will try with the above suggestions.

Hi Nicola Piasentin Thanks for the above my problem of ions is solved. I did it manually as per suggestions.

I am seeking for your help further to reduce the time of MD

When I am writing command for MD simulation (100ns) (gmx mdrun -v -deffnm md_0_100) it showing it will finish in approx 30 days, and I am getting a message. Can I reduce the time of simulation??? My system is i7 window 10 RAM 16 GB and graphic card 2 GB nividia.

This is the message which i am getting during MD

gmx mdrun -v -deffnm md_0_100

Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).

The current CPU can measure timings more accurately than the code in

gmx mdrun was configured to use. This might affect your simulation

speed as accurate timings are needed for load-balancing.

Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.

Reading file md_0_100.tpr, VERSION 2020.1-Ubuntu-2020.1-1 (single precision)

Changing nstlist from 20 to 80, rlist from 1.222 to 1.319

Using 1 MPI thread

Non-default thread affinity set, disabling internal thread affinity

Using 8 OpenMP threads

WARNING: This run will generate roughly 2431 Mb of data

starting mdrun 'Protein'

50000000 steps, 100000.0 ps.

step 262000, will finish Fri Oct 2 17:15:54 2020

Hi Pankaj Bhatt ,

Sorry I can't help you more. The run time depends strongly on your computer specifics, and usually personal computers are not great at all and you must rely on clusters. PCs are useful in the limit or energy minimization/analysis/short runs of small systems, nothing more (and even in this case they can take up to days of computational time).

The only thing that could help you is using your GPU to ease the computational load, if you are not already doing it. I am not expert on this, but you should easily find what you need, like this page is a good starting point

http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html

Nicola Piasentin Thanks for your suggestions.

Kunal Dutta