[gmx-users] LJ-14 energy

Ming Tang m21.tang at qut.edu.au
Thu Jul 16 13:24:24 CEST 2015

Dear Justin,

1.  The total Lennar-Jones 12-6 energy of the whole system is the addition of LJ-14, LJ-SR and LJ-LR. Analogously, the coulomb energy is the addition of coulomb-14, coulomb-SR and coulomb-LR. Is my understanding of your explanation right? Besides, in Gromacs, is the potential energy the addition of G96Bond, G96Angle, Proper-Dih, Improper-Dih, LJ-14, Coulomb-14, LJ-SR, LJ-LR, Coulomb-SR and Coulomb-LR?
You are right. That's why I don't get the LJ-LR and Coulomb-LR options when using g_energy. Suddenly, I realised that my understanding of the twin-range approach was totally wrong. For cutoff-scheme = verlet, rlist cannot be smaller than rvdw = rcoulomb, and When using twin-range method, either coulombtype = cut-off with 
rcoulomb ≥ rlist or vdwtype = cut-off with rvdw ≥ rlist. Does this mean that for twin-range approach, rlist = rcoulomb = rvdw when cutoff-scheme =  verlet? However, even if I set vdw-modifier = potential- switch, the rlistlong larger than rlist is reset to be equal to rlist by gromacs, and there is not LJ-SR option when using g_energy. I am totally lost. Can you help to tell me how does twin-range work when cutoff-scheme = verlet?
Another question is I used the following code to make my cut-off parameters be consistent with those used for the triple-range cut-off scheme in the paper defining Gromos 54a7 force field:

coulombtype      =  reaction-field
coulomb-modifier =  potential-shift
rcoulomb-switch  =  0.8
rcoulomb         =  1.4
epsilon_rf       =  61

Currently, I think it is wrong. It seems that rlist = 0.8 is reasonable. But rlist should not be smaller than rcoulomb when cutoff-scheme = verlet. How to achieve this triple-range cut-off scheme?

2.   The pull rate I use is 4e-5/ps. I thought it is small so that the energy of water can be treated as constant during the pull process. I forgot to consider the water-protein interaction and that my pull rate is much larger than the pull rates used in the experiments which is in order of micrometre per second and is much more relevant to physiological pulling rate. You are right, I cannot treat the trends of the system's energy as those of the protein's energy. But how can I get the energy of the protein? Is it feasible to set all the atoms of the protein as one energy group, and do rerun to achieve this?

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Thursday, 16 July 2015 11:20 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] LJ-14 energy

On 7/15/15 8:39 PM, Ming Tang wrote:
> Dear Chaban and Justin,
> Sorry for the mis-action. Please ignore my last email.
> Thank you both for your free help.
> I am pulling a collagen triple helix in a periodic water box using 
> umbrella direction-periodic. I want to calculate the Lennard-Jones 
> 12-6 of the protein. According to Gromacs manual, it contains 
> repulsive short-range term and attractive long-range term. Is the 
> Lennard-Jones 12-6 energy simply the addition of LJ-SR and LJ-LR? I am 
> interested in the energy trends more than

LJ-LR only exists with a twin-range cutoff approach.  The total LJ between any groups also includes LJ-14 for intramolecular terms.  Intermolecular LJ would be the sum of LJ-SR and LJ-LR, if the latter exists.

> the energy absolute values. So, if I can calculate the LJ 12-6 of the 
> whole system, it is fine, because I can assume the energy of the water 
> is not subject to change due to pulling.

Why can you assume that?  You're pulling a structure, which is a non-equilibrium process.  There will be different interactions as a function of time. 
Water-water interactions at long distance from the protein indeed are unlikely to be affected, but those close to the protein may be different (though electrostatics/hydrogen bonding are probably much more interesting). 
Water-protein interactions certainly can't be assumed to be unchanging during pulling.



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

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