Entering edit mode
6.7 years ago
marco23.p ▴ 20
Molecular Dynamics: I have found tons of examples of molecular dynamics with GROMACS with fully aqueous solutions. This time I need some advice about simulating a system that is, say, in a solution with X% of Acetic Acid.
Any hint on how to proceed?
Sorry for my newbishness on the argument but I've jumped on this topic (MD) right in the last few months (I'm coming from RNA structural motif discovery so... be kind :D)
Take a look at http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
So, let me get this straight, because it seems a little bit shady to me:
I calculate that given the box type I choose right? (if I choose rhombic dod and I need 20% AA I just need to make calculations, correct me if I'm wrong)
that's gmx pdb2gmx, so I assume I must find a .pdb of my co-solvent single molecule
Do I need something like this for my .itp? :
;;;;;; ACETIC ACID
; molname nrexcl
; id type resnr residu atom cgnr charge
1 P3 1 ACH OOH 1 0*
Thanks for the help, much appreciated
Not only the box type. The -d option of gmx editconf changes the box size as well. The stdout output from gmx editconf shows you the box size, volume, diameter, etc.
Yes, just run gmx pdb2gmx. Remember to save the acetic acid .itp file produced here. The default output name is posre.itp but you can change it using the -i flag.
You need to include the .itp file for acetic acid in your topol.top file. Something like that should work:
The position of this line in your topol.top is important. You probably need to put it right after or before the lines that include the water topology (; Include water topology, etc).
You also need to add a line at the [ molecules ] part of your topol.top. It's in the end of topol.top. Example:
If 'ACH' is the name for acetic acid in your original pdb file.
GROMACS 5.1.2 split gmx genbox into gmx solvate and gmx insert-molecules. I would probably first use gmx insert-molecules to add the acetic acid and the run gmx solvate to fill the remaning of the box with water.
Ok good, I just ran into a doubt today. I obviously need force-field parameters for acetic acid right? otherwise pdb2gmx cannot create a topology, can he? Or well, I'm sure he can, but that would be utterly wrong I think
Thank you for your answer, I'll be trying that out in days and get back here.
I'll Leave this open until I solve this problem, if anyone wants to add anything, well that is welcomed
You can use PRODRG to generate the topology, as they did here.