[gmx-users] LJ-14 energy

[Ming Tang]

Dear Justin,

Thanks very much for your explanation, my confusion on LJ energy has gone now. Besides, thank you for telling me my assuming is incorrect.

Regards.

-----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 9:50 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] LJ-14 energy



On 7/16/15 7:08 AM, Ming Tang wrote:
> Dear Justin,
>
> Thanks. 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

Well, that's the exact definition of an additive functional form, so yes.

> 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?
>

I honestly have no idea.  I don't use GROMOS force fields any more.  With the group scheme, it is easy, but with Verlet I have no idea what the equivalent approach is.

> 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?
>

The energy of the protein is not a useful quantity.  It is a force field-specific quantity.  Energy differences and free energies are valuable.

-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

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