A question about gen_seed in the log file

User discussions
, ,
1

GROMACS version: 2018.8
Hello,
I am using the COM pulling options to do the pull simulation of my system. I want to do several identical pull simulations from the same configuration but with different initial velocities. In my understanding, these are identical simulations of different starting microscopic states. In this way, I can improve the statistics of my output data.
So, I am trying to explicitly set different gen-seed to generate different initial velocities of the same configuration. But I am a little confused that I checked the log file, in the section input parameters, I only found that the line of ld-seed is different from my different simulations. I did not find a line that contains gen-seed in the log files. As a result, I am not sure whether my setting of gen-seed is effective in my simulation. How can I check whether a different gen-seed has been successfully set?
It seems ld-seed is a different thing, but I am not sure what is the effect of this parameter on my simulation, if a little more explanation could be given for this parameter, that would be much appreciated!
Thanks very much in advance!

2

Check once with generated mdp file whether u face the problem.

Use option gmx grompp -po option to get mdp file.

3

You can obtain its value from gmx dump or the actual velocities themselves. The velocities in each .tpr file will be different.

4

Thank you very much for the reply!
The default output .mdp file of gmx grompp seems to be mdout.mdp. I found that gen_seed is included in the mdout.mdp file. Do I understand correctly what you mean?

5

Thank you very much for the reply!
Your suggestion exactly matches what I need. gmx dump can print the information of velocities on the screen.
After consult the doc page of gmx dump, one minor problem I found is that, it seems the command does not give an option to output the information to a file. I have 30000 atoms, then it becomes very hard to browser all the information, I only can view the last part of the output on my screen. Could you please give me more help?

6

May be it is sloved already.
You can use, gromacs commands > output.txt
“>” (or “>>”) help to write output from screen to a file which can be used for future purposes.

7

Hi, thank you very much for the reply!
That is exactly what I need. To redirect to an output file would just solve my problem, I should have thought about this before. Thanks very much!