[gmx-users] LJ-14 energy
vvchaban at gmail.com
Wed Jul 15 15:22:41 CEST 2015
On Wed, Jul 15, 2015 at 6:27 AM, Ming Tang <m21.tang at qut.edu.au> wrote:
> Dear Gromacs experts,
> I am confused about the meaning of LJ-14 option in g_energy. I checked the achieve, and found that Justin said it stands for intramolecular interactions between atoms separated by 3 bonds. My simulation is protein solvated in water. How can I calculate the Lennard-Jones potential energy of the whole system?
> I found that if I set 2 energy groups and rerun, there will be options like LJ-14: protein-ions. So, how does Gromacs calculate those energy?
Yes, LJ-14 is an intramolecular term. It may be simpler to exclude
this term from summation when calculation total energy. If you exclude
it for one system, then obviously exclude for all other systems you
> Another problem I came across is the LJ-14 I got is weird. The Coulomb-14 energy decrease from 5e4 to 3.8e4, but LJ-14 energy decrease from -400 to -700 and then increase to- 400, followed by a linear decline to -1700. The LJ-14 should increase, am I right?
This fully depends on which objects you have in your system. Upon
which action do these terms increase?
> Here is part of my .mdp
> cutoff-scheme = verlet
> ns_type = grid
> coulombtype = reaction-field
> coulomb-modifier = potential-shift
> rcoulomb-switch = 0.8
> rcoulomb = 1.4
> epsilon_rf = 61
> vdwtype = cut-off
> vdw-modifier = force-switch
> rvdw-switch = 0.8
> rvdw = 1.4
> To find out the reason, I checked the manual. It says for vdwtype = switch or vdw-modifier = Potential - switch, rlist should be 0.1 - 0.3 larger than rvdw. As I did not set verlet-buffer-tolerance = -1, gromcas set rlist =1 for the simulation automatically, which is not 0.1 - 0.3 larger than rvdw. Is this the reason of the weird LJ-14?
> Another question is, is vdw-modifier = force switch more accurate than vdw-modifier = potential - shift?
> Any help will be appreciated.
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users