GROMACS version: 2021.4-Ubuntu-2021.4-2
GROMACS modification: No
Hi everybody,
I want to simulate the reaction of a molecule on a rigid gold surface in gromacs.
That is why I used the GolP force field and initialized my start cell with the gold atoms and the connected molecule. The topology file was then structured that I repeated the start cell as often as I multiplied it in the coordinate file instead of just calculating the amound of atoms and writing it down. This way the layer was rigid, but it slowed down and had errors in the simulation.
Now I tried to used the total of the atoms/molecules in the topology file (so just 2 rows instead of the amound of multiplications) but this way the layer is not rigid and the atoms are moving to one side.
My solution approaches:
added the lines for freezegrps and freezedim for the depending group, the gold, in the .mdp file. Nothing happened.
freezegrps = AU
freezedim = Y Y Y
added the lines for restraints in the depending .mdp files. Nothing happened.
define = -DPOSRES
And the following lines in the .itp files.
[ atoms ]
1 Au 1 AU AU 1 0.0
[ position_restraints ]
; i funct fcx fcy fcz
1 1 500000.0 500000.0 500000.0
Does anyone knows what is missing and why nothing is happending?
Sorry if it is obvious, this is my first big simulation and I got nothing helpful from tutorials or other threads/questions what solved my problem, although I found this kind of question a few times.
Kind regards,
Konsti
PS: If anything more is needed please ask. I just thought that this is enough information for a general overview and maybe even tips to solve it mysef.
Could you please report the kind of error that Gromacs is throwing?
Why are you using “define -DPOSRES”? As far as I understand it is not needed to declare position restraints. Also, one small remark: ‘freezed’ and ‘restraned’ are not the same thing; what do you intend to do (physically, I mean)?
there is no error, the simulation is running, just the result is not what I want it to be.
My goal is to have a rigid metal surface layer (that is why freezing the atoms is an option too, I read that for rigid surfaces this is a possibility) with molecules stuck to it through a covalent binding.
The next step then is a rigid surface layer and the same molecule but in the simulation box above the layer and below empty space.
So first I need a rigid layer. First I used this structure with the GolP force field and the layer was rigid:
AU 4
ABNG 1
…
(Times)
…
But with a specific molecule size “gmx mdrun -deffnm pr” does not work anymore so someone mentioned that it might be easier for gmx if I sum up the amound of atoms and molecules in the .top file and not mention every cell for it’s own. So now the structure is like this and the rigid structure is gone. That is why I am trying to solve this with restraints or freezing.
AU 4000
ABNG 1000
Kind regards,
Konsti
PS: I forgot to answer your question why I am using the “define=-DPOSRES” command line. I just thought, that to use position restraints you have to decide if you want to use flexible or restraints molecules/atoms and set this variable. Of course, if I freeze the atoms I do not need the “define” statement, but neither do I need it if I use the restraints??
You need list the number of all the molecules in each group in the topology file. That is, if you consider a single gold atom as a molecule (in the Gromacs sense, not in the ‘chemistry’ sense), you need to write the total number of gold atoms per box in the topology file. If the position_restraints directive is in your topology file (or included in it via #include), it will be considered automatically without the need of -DPOSRES.
Thus said, why is the simulation not working in the first place? What do you mean by “nothing happened”? Are the gold atoms moving? Restrained molecules can still vibrate because of thermal fluctuations (frozen molecules on the other hand are completely immobile).
ah good to know, thanks! I will try it till tomorrow and let you know if it worked. :)
With “nothing happened” I meant that the gold atoms are not just moving a litte bit (like they could if they were restrained), but through the complete simulation box. Even if I set the restraints very low. So I just meant, that the restraint is not working. Nothing happend in case of position restrictions. But I hope it will work if I include all gold atoms in the topology file or in a posre.itp which is included in the topology file.
Yes, I know that if you freeze them, they can not move a bit. But I mean in case of a rigid layer this would be okay I think.
ABNG should just be any kind of molecule. In my simulation I want to use different ones, so I just typed on my keyboard wildly four letters. :D
I want to use HCN7 for my simulations as an example.