[gmx-users] Total energy with different energy groups

Daniel Cheong dcheong at ihpc.a-star.edu.sg
Tue May 29 03:00:57 CEST 2007

Hi Mark,

Thanks for all your replies and suggestions!  I really appreciate it.  

The observations are indeed inconsistent and that is why I am quite 
confused.  I am not changing anything in my mdp file except for the 
energy groups.  I literally use the same file and just add/change/remove 
the line for the energy group, save the file and run the calculation 
again with a different output filename.  I don't even touch any of the 
cutoff or neighbor list generation frequency or any of the other 
parameters.  In fact I am not even running any MD on it.  I am just 
calculating the initial energy of the configuration.  Hence my surprise 
when I find the total and non-bonded energies turn out different.


Mark Abraham wrote:
> Daniel Cheong wrote:
>> well...  the bonded energies are the same, but the 1-4 and nonbonded 
>> interactions are different, especially the coulomb-sr energy.  I am 
>> using a direct summation method with no cutoffs to calculate the 
>> electrostatic energy.  But the method is consistent between the 
>> runs.  So that shouldn't matter should it?
> Your observations are inconsistent. 1-4 interactions should be just as 
> reproducible as bonded ones, since they too depend only on the 
> topology and configuration. If the other non-bonded interactions 
> aren't reproduced then I can only suppose you are also changing your 
> cut-offs, or neighbour list generation frequency or some such. Use 
> diff on your .mdp files. Use mdrun -rerun.
> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before 
> posting!
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

This email is confidential and may be privileged. If you are not the
intended recipient, please delete it and notify us immediately. Please
do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.

More information about the gromacs.org_gmx-users mailing list