Dear researcher,
I want to simulate my protein with the denaturants (MW-139 Da). I am using Gromacs 2018.2 version and the extra molecules were added by using gmx insert-molecule command.
I want to add different concentration of denaturants like 10, 20............. til 90%. I have successfully added the 20% denaturants in the simulation box and run the simulation while I want to add more than 20% so the command adds a particular number and terminate with a massage (2241 is successfully added out of 3271 requested).
I have increased the box size so the number of denaturants were also increased due to increase of water molecules, so problem is same. I also read the gromacs mailing list but i can not find any solution.
Please suggest me how i can add the total molecules in the simulation box.
Thanks for your response in advance.
What do you mean by 20%, 1 molecule of the denaturant per 4 water molecules?
I have faced a similar problem before where it fails to insert the number of molecules I want into the box. You might want to play with the "-try" flag for gmx insert-molecules. The "-try" flag tells it how many times and configurations you want it to try per molecule. By default, it tries 10 times. I increased it to 50 "tries" per molecule added and it worked. For example, I wanted to insert 10 molecules into a box with the -try 50 flag, so it would try inserting each molecule up to 50 times with a maximum of 500 (50*10) attempts.
You can also use the "-rot xyz" flag so that it tries random rotations. I have also found that to be helpful.
edit: more detail, typos
Thanks Martin Klvana and JD Tamucci for your quick response. The problem is solved with try 50 flag.
Thanks again for your help.
- Badges
- Science topic