[gmx-users] LJ-14 energy

[Justin Lemkul]

On 7/15/15 5:27 AM, Ming Tang 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?
>

Intermolecular LJ-14 are by definition zero and actually do not correspond to 
anything real, anyway.  Just a quirk of the decomposition of nonbonded terms in 
the code.

> 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?
>

Depends on what's happening.  There's no reason to think that any energy term 
will inherently show any trend, but the outcome reflects whatever is happening 
in the dynamics.

> 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?

I think you're mis-reading the manual.  If you set verlet-buffer-tolerance = -1, 
whatever value of rlist you specify (which you haven't shown, so it defaults to 
1) is used.  You say you did *not* set verlet-buffer-tolerance explicitly, so it 
defaults to a value of 0.005 and rlist is tuned as needed.  The .log file will 
have information as to what rlist was used.

> Another question is, is vdw-modifier = force switch more accurate than vdw-modifier = potential - shift?
>

The method used depends on what the force field needs.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================