You should ask this to YASARA support team,

You can load the scene and last frame-> then run the macro

Dear Shir Nee Ong,

It's pretty simple and quite helpful for molecular dynamics (MD) simulation through YASARA to initiate the simulation where it was ended.

Step 1. Open YASARA> file> load> YASARA Scene> your desire folder and select water.sce file and press ok.

Step 2. Options> Set target> your desire folder and select your .sce file and press ok

Step 3. Options> Play macro> select your desire macro file

After that this MD simulation will start again from where it ended.

But I have a concern about how you incorporated thirty percent ethanol as an alternative to water on the solvent phase in the simulation box? Shir Nee Ong

Md Ackas Ali Thanks for the answer will try to do so. For the 30% ethanol part, I loaded the sdf file into the simulation, then I fill the cell with copies of an object (which is ethanol) until it reaches the final density (For example, 30% of ethanol will be 0.7893 *0.3= 0.2367). The water will be (0.7*0.997=0.6979)density. From the macro file, I change the final density of the simulation into (0.2367 +0.6979=0.9349). Then I run the macro file as usual.

I also have doubts about this simulation protocol as provided by my senior colleague. But throughout the simulation, the ethanol remains in the simulation and the solvent density does follow the one I input into the macro file, it's just that the water content increases drastically when I run the simulation. Feel free to point out if you have found any mistakes in the protocol I stated above. Thanks

Shir Nee Ong, I wonder about the protocol you are using because as far as I know about Yasara Molecular Dynamics package, the default macro adds water maintaining a specific density which is not physicochemical solvent density but the density of the simulation box. In that case, it's better to calculate the density in terms of the number of molecules so that the dynamics protocol get clear information about the required percentage of co-solvents.

Thank You.

Mousumi Saha Ah then it makes so much sense because, in the end, it added so much water during the simulation. If in that case, I will try to check the number of molecules for the solvent then. Thanks for the input!