Molecular Dynamics in Acetic Acid
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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)

MolecularDynamics AceticAcid Buffer ProteinFolding • 2.8k views
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So, let me get this straight, because it seems a little bit shady to me:

Determine the number of co-solvent molecules necessary, given the box dimensions of your system.

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)

Generate a coordinate file of a single molecule of your co-solvent (i.e., urea.gro).

that's gmx pdb2gmx, so I assume I must find a .pdb of my co-solvent single molecule

Use the -ci -nmol options of genbox to add the required number of co-solvent molecules to the box.

ok

Fill the remainder of the box with water (or whatever your other solvent is) using genbox.

ok

Edit your topology to #include the appropriate .itp files, as well as make changes to the [ molecules ] directive to account for all the species in your system.

Do I need something like this for my .itp? :

;;;;;; ACETIC ACID

[moleculetype]

; molname nrexcl

ACH 1

[atoms]

; id type resnr residu atom cgnr charge

1 P3 1 ACH OOH 1 0*

Thanks for the help, much appreciated

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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)

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.

that's gmx pdb2gmx, so I assume I must find a .pdb of my co-solvent single molecule

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.

Edit your topology to #include the appropriate .itp files, as well as make changes to the [ molecules ] directive to account for all the species in your system.

You need to include the .itp file for acetic acid in your topol.top file. Something like that should work:

; Include acetic acid topology
#include "aceticacid.itp"


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:

[ molecules ]
; Compound        #mols
Protein_chain_A    1
SOL             1000
ACH              200


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.

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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

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You can use PRODRG to generate the topology, as they did here.

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