Molecular Dynamics basics!!!!!!!!

[MDnovice]

Hi,
if anyone can help me I would be very grateful.

I am not quite sure about some terms in Molecular dynamics (MD) and even after running the simulations and looking at the output it still remains unclear. I am using the MD package called DL Poly ....... but my questions I think are general to any MD simulator ...

1) what is the relationship between steps, time step, job time and close time? say i set the simulation for 500 steps and timestep of 30ns shouldnt that mean and the total simulation time is 15000ns?.... because if I set the job time for say 10 min, the simulation will run for 10 min ? isnt that right? (as for closing time I dont know what it means)

2) with a thermosat and a barostat (when running in NPT for example) , what does relaxation time mean ? and how do I use it? ?


thank you very much in advance

[BioWizard]

I might be able to help with some of that.

1) what is the relationship between steps, time step, job time and close time?

A step refers to the length of simulation time before the new coordinates are calculated and written. The longer the step time, the less "resolution" your simulation will have. If you define your step as 10 fms, your simulation will write coordinate files at a frequency 10 times higher compared to a simulation with a step of 100 fms. Job time, I assume, is just the time that the computer takes to run the simulation job. This is dependent on the specs of the machine running the simulation. Close time, I'm not sure about. It might just be a cut off time, which if the simulation is instructed to terminate the simulation if it goes over it.

say i set the simulation for 500 steps and timestep of 30ns shouldnt that mean and the total simulation time is 15000ns?

That is correct.

.... because if I set the job time for say 10 min, the simulation will run for 10 min ? isnt that right? (as for closing time I dont know what it means)

Yeah, I'm not sure either.

2) with a thermosat and a barostat (when running in NPT for example) , what does relaxation time mean ? and how do I use it? ?

I can't remember what relaxation time stands for, but it might be the time allowed to the system to relax/equilibrate if it's temperature or pressure go over what you set them to be.


thank you very much in advance[/quote]