Solvent-Water-reg

[GJK]

We can do MD simulation using ATK.
Is it possible to provide a script to find solvent interaction studies ??
We can calculate up to dipole moment which is directly related to Gibb's free energy of solvation.

I tried to run my scripts optimized in ATK and having done the dipole moment calculations to run using Gaussian 2003 for predicting solvent interaction. But the compatability failed in Gaussian whereas ATK provides the compatibility.

Since I papers where people have worked up to gas phase dipole moment calculations using ATK.having the MD simulation if you could provide solvent interactions we(medical physiscts researchers) will be highly grateful

[GJK]

Your valuable suggestions are highly appreciated

[Jess Wellendorff]

Please allow us time to carefully consider your questions before answering.

[Anders Blom]

Based on your information above, it's not clear at all what you mean. Besides, I don't think one can just provide a script than enables an entire study on any topic. If you have a question on how to perform a specific task, we can help, but to design an entire framework for simulations is more complex and requires a good understanding of the topic, and I don't even understand what kind of atomic system you are interested in.

[GJK]

Dear Prof.Anders,

We are doing solubility studies for nanocarriers using graphene as the base material.To test the solubility we need to check whether the material has dipole moment or not. In ATK we have done up to dipole moment calculations but for solubility we need solvent as a medium.We tried our ATK optimized system for solubility studies alone using Gaussian 2003(it has solvents). But it is not compatible.ATK is user friendly.

In the recent post named "liquids" I found that we can perform MD simulations with our optimized systems by using around few water molecules.If you could provide the unlimited solvent base(ATK with both gas phase and different solvent phases) it would be helpful for us (medical physicists,chemists) to provide reasonable results for drug carriers which is very important with respect to saving life's of diseased people.

Thanks in advance

[Anders Blom]

What does "unlimited solvent base" mean? Any molecule as solvent? If you use DFT you are not limited in this respect, and most small organic molecules can be described well by say ReaxFF which is in ATKClassical, so this is already possible.

[GJK]

What does "unlimited solvent base" mean? Any molecule as solvent? If you use DFT you are not limited in this respect, and most small organic molecules can be described well by say ReaxFF which is in ATKClassical, so this is already possible.

"Unlimited solvent base"- use solvents freely without constraints restricting to 100 or 50 in number (like what was answered under Liquids query you can use 50 or 100 water molecules using MD"

Kindly provide us scripts if possible for finding the interaction between a solid system and solvent system and hence estimate the Gibb's free energy of solvation.

Thanks in advance

[Anders Blom]

No such constraint exists in ATK, it was just an example, 50, 75, 193, 2445, use as many molecules as you want/need/have capacity for in your calculation. Of course with DFT you are much more limited, but for a classical force field you can use 100,00 atoms if you must.

[GJK]

Hi ,

Is it possible to implement implicit solvent model (like PCM,COSMO) and hence determine the free energy of solvation both in gas phase and solvent phase???.This is what actually I mean.

In ATK we can manually add some water molecules optimize using geometry optimization and MD to find the stability and interaction.But we can't find the solvation energy since the solvent models (implicit) not been incorporated.

Your valuable comments are highly appreciable for medical community to use ATK .

[zh]

As far as I understand  that the solvation energy estimated by PCM and COSMO model is strongly dependent on the values of some key parameters (such as the dielectric constant function of implicit solvent) in the model. The explicit treatment of solvent by including in the water (or other solvent) molecules in the molecular dynamics simulation is more reliable. The issue is the increase of computing cost. The solvent energy can be estimated by the MD simulations without and with solvent molecules.  For example:

without solvent
system: A + B,   A is the substrate, B is the adsorbed molecule;   
 their interaction energy  between A and B (or adsorption energy of B on A)  =  E(A+B) - E(A) - E(B)

with solvent
E(A+B+ solvent)  - E(A) - E(B)- E(sovlent)

The solvent energy (i.e., the effect of solvent on the adsorption of B on A) :   E(A+B+sovlent) - E(A+B) - E(solvent).