Currently I'm trying to solvate a protein with a ethanol-water mixture I made and equilibrated.
I did as this page says http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
with a box of 3 nm each side, added the ethanol molecules and solvated it with water, followed by energy minimization and NVT->NPT equilibration during 50 ps.
But when I try to use the .gro file that resulted from the equilibration to solvate my actual system (gmx solvate -cp protein.gro -cs mixed_solvent.gro -p topol.top -o prot_solv.gro), the program tells me the solvent atoms added, the atoms removed due to overlap with the protein, that it found 2 molecule types in the solvent and how many atoms each one, followed by:
*** Error in `gmx': free(): invalid pointer: 0x000[...] ***
ending with an abortion mesage of core dumped.
I once was able to use mixed solvents by adding to the protein system the whole amount of molecules needed for the box volume.
But as I moved from using a cubic system in the production simulation now it's more complicated to calculate the volume (as I'm using -d instead of -box in the editconf) in adition to being a little afraid the mixed solvent might not be properly equilibrated if I just add randomly a bunch of ethanol molecules and hope for the protein+solvent equilibration do the job.
The .gro file for my mixed solvent has different residue numbers for every molecule regardless of it being water or ethanol, and the ethanol atom names are CAA, CAB, OAC, HAF. But since everything worked when I solvated the ethanol with water I'm sure there's something I'm missing between the npt equilibration and the protein solvation
If someone has any idea of what might be my fail, please let me know.
Hi Nebojša, thanks for your answer.
That was the way I was doing it at the beginning, when I was using a cubic system. But I moved from cubic to a dodecahedron, and I don't give it the size of the box, I only tell the program to fit it so there is a "d" distance between all the sides of the box and the nearest atoms of the protein. So I really don't know the volume of the box. That's the reason I was trying to use gmx solvate, as it's mentioned in this other question by one of the GROMACS developers:
https://www.researchgate.net/post/How_do_I_add_urea_as_a_co-solvent_in_gromacs_molecular_dynamics_simulation
I will give packmol a try then and tell you how it worked.
Why do you think I don't need to pre-equilibrate the mixture?
I decided to do it as I read in many places to use pre-equilibrated solvents, as well as it was a recommendation I got in a class, so I find it interesting to know how much of it is actually helpful and how much is just mannerisms
Hello Stéphane,
Thank you very much
I have read in a couple of places to use gmx solvate for mixed solvents, so I was hoping the problem was in something I do instead of the program not being able to do it.
I will follow your advice, maybe if I generate a solvent box big enough to be biger than my protein box then I can use gmx insert-molecules to overlap both boxes and hopefully his way the program is gonna work. If not, I would have to go back to using a cubic box with known size, but I'm trying to avoid having to simulate the solvent in the corners of such box type, as I don't have too much compute power (so maybe I will also test generating a dodecahedric solvent box and insert the protein in it after that)
I'll update how it worked for me in the case other RG users find it useful in the future.
Can you tell me how to calculate no. of molecule for a particular concentration (e,g. 8 M urea) for a dodecahedron box.
Hello, to all future viewers of this question.
As recomended by Nebojša I used the packmol. Then I was stoped by gromacs not recognizing the molecules in the output from packmol. After a while I achieved to change the id of the atoms in the files coming from packmol so they were recognizable by gromacs and everything ran smoothly. I did it on the plain text file, changing the ethanol name to ETHH and the atom ids to EC1, EC2, EH and EO, as I found were the ids in the gromacs residues files that come with the program.
I decided using a sphere after all, but promising myself one day try to lear how to use more geometries just in case I need it someday.
Thanks to everyone, and hope this helps someone in the future.
Krishna, you just have to calculate the volume of the dodecahedron given the size of every side if you know them, if not, maybe measuring it in a molecular visualization tool such as pymol. I tried to do that as I didn't know the exact size of the dodecahedron because of using -d 1.0 in the options. But got frustrated and preferred doing the sphere of known radius in packmol.
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