In one journal I read the real pressure was 25MPa, but in MD simulation, they applied 18.6MPa only. In my study, I used 10MPa but I don't know how to predict the pressure in MD simulation? Thankyou for your suggestions and help.
Hi,
- Most packages provide a barostat, which is a feature varying the cell volume and thereby controlling the pressure. The use depends on your package, and just as for the thermostat, there may be different algorithms, starting with the Parrinello-Rahman dynamics.
- In condensed phases, the important parameter is usually the density rather than the pressure. You may want to check, if your force field correctly reproduces the experimental density at the given high pressure.
Do they controlled the pressure to be 18.6 MPa or it was that number? If the have used NVT ensemble so they have no control on the pressure of course, but if they have used NPT ensemble and applied lower pressure, the questionis "why?". My first guess is the deficiency of the force field they have used (this is a trick to get a correct density as Walter Langel mentioned.). Otherwise I don't see any reason to do such thing.
from journal, they used both NVT and NPT. but since they controlled the pressure at 18.6MPa, they might used NPT as an ensemble. but this is not a real pressure as in their experimental work since in real they used 25MPa. in my work, i controlled the pressure at 10MPa but i didn't know how to estimate pressure in MD simulation. and i have problem also in determining the density since it is difficult to determine at high pressure and temperature during my experimental work.
Gas or solid media?
If the volume of your computation area is fixed, you can only change temperature or density in MD simulation. Temperature can be maintained by thermostat (for example through the velocities scaling). Density - through variation initial molecules number.
the system is liquid form. coz applied bioactive compounds in water at elevated T and P. i didn't fix the volume only control the pressure. now, i am trying to find the pressure which by setting the density (nvt) of water only. once the pressure (water only) was found, i proceed with the same pressure to real (bioactive+water). but i found that pressure is too low about 4.6 atm. the experimental work is 102 atm.
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