Author Topic: FROG module  (Read 2135 times)

Olynes

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FROG module
« on: January 15, 2015, 04:37:49 pm »
Hi All,

I've recently started using the FROG module in TURBOMOLE in the hope of using it to do some molecular dynamics calculations. I don't have any issues using the frog module, however if I run the job more than once it's giving me the same trajectory each time, even when I've specified a completely random velocity. 

My understanding was that molecular dynamics was moving towards more realistic behaviour, so if the same calculation is producing exactly the same set of co-ordinates each time it's run that is unlikely to be realistic.

Is there a selection in mdprep I'm missing which would allow me to run a multiple molecular dynamics calculations which are each random on the same structure?

Many thanks


uwe

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Re: FROG module
« Reply #1 on: January 16, 2015, 10:03:44 am »
Hello,

when preparing a molecular dynamics run with mdprep you get through a couple of menus, the option to generate a random MD job can be found in the 'initial velocity' menu:

  • NUMBER OF ATOMS
  • Cavity Barrier Attributes:
  • Distance Constraints:
  • INITIAL VELOCITY

...................................

     INITIAL VELOCITY
. . . . . . . . . . . . . . . . . .

Assigning random velocity, with KE about  0.475065000000E-02
     representing a temperature of about   500.000000000

Current status of INITIAL VELOCITY
random velocity at temperature of   500.000000000     K

Enter option:
     d  Default: random velocity at temperature of   500.000000000     K
     i  Interactively enter temperature for random velocity
     z  Zero velocity
     r  generate non-reproducible random velocity
     h         Help
     &         Back to previous menu and reset
     q or '*'  Terminates this menu ('qq' to abort <mdprep>)


The default is here to set a random velocity which leads to reproducible MD simulations. If you want to generate different random MD jobs, choose the option 'r' here: generate non-reproducible random velocity

Alternatively, generate one MD input, make copies of it and change the seed for the random number generator to different values. Edit the file mdmaster and change the line:

$seed  788428536

If you do it on the command line using e.g. bash, you could use the build-in random number generator by using the environment variable $RANDOM.

Regards,

Uwe