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.
Daniel
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 [email protected]
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 [EMAIL PROTECTED]
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.
----------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
