Re: [ESPResSo-users] setmd time and rg

[Stefan Kesselheim]

Hi Roya,

On 07.05.2014, at 08:45, roya moghaddasi <address@hidden> wrote:
 
I'm not familiar with the analysis set chains syntax, so maybe someone else 
could check it ...

>   I ran my program twice, the first time "setmd time" gives me 499.5 to 
> 5449.5 through 10^6 step, the second time it gives me 2449.5 to 7399.5, why 
> this happens? I thought it should start with the same number and it ends with 
> the another same number each time I run the program since there is no change 
> in my program.

That depends on what you did before these lines. [ setmd time ] yields the 
total simulation time (n * time_step, if the time step was constant) until that 
very point.  If you use, for example, a warmup method that does not always use 
the same number of MD steps, you get different [ setmd time ] for different 
runs.

> Another question is there are fluctuations in the rg  value, in other words 
> it fluctuates between 10 and 11 a lot and in second run it reaches to 14-15 
> value from 10-11 value, I am so confused, what does these results mean? why 
> does the value of rg changes in each run, is there any mistake that I made?

rg is a fluctuating quantity, that depends on the conformation of the polymer 
(you could say, rg describes how extended a certain polymer conformation is). 
You probably want to obtain the mean value, which people tend to call the 
"radius of gyration of a polymer".

There is probably some difference between your two runs, that you have not 
mentioned. Try to run shorter runs first and see if they do what you expect and 
only go to longer runs, once you are happy with the results of short runs. 
Simulation business is always iterative, because the scripts you write always 
have bugs, and it takes some time to get rid of them.
Cheers
Stefan