Looking at NAMD or GROMACS manual, for example, is very well explained (and easy top use) how to set up thermostat and/or barostats to simulate your system as NVE or NPT
thanks for your help. but i need the description of the algorithm. i found that in computer simulation pressure has been set with Clausius theorem. could you pleas explain it for me?
You can find information about the Clausius theorem and the virial theorem in their respective wikipedia pages. You might also find the following lecture on MD simulations useful (it includes a sub chapter on pressure):
However, it would be easier if you just told us what MD suite you have been using and which pressure control method you have employed, so that we could direct you to more specific sources on the algorithms.
In any case, one of the most widely used pressure control methods, particularly for GROMACS users, is the Berendsen barostat. You can find the original paper describing their pressure coupling control method in this link:
Most NAMD users, on the other hand (myself included), usually work with Langevin dynamics for temperature and combine it with the Langevin piston method, which is essentially an adaptation of the Nose-Hoover algorithm (originally designed for temperature) to pressure control. The paper of the method is in the following link: