[gmx-users] LJ-14 energy

Thu Jul 16 02:40:09 CEST 2015

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 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.

Thanks.

-----Original Message-----

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se<mailto: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: Wednesday, 15 July 2015 11:36 PM

To: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>

Subject: Re: [gmx-users] LJ-14 energy

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.

-Justin

This does make sense! Your explanation is always clear and precious. I found that LJ-14: protein-ions of my system is really zero.

> 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.

-Justin

I did not set value for verlet-buffer-tolerance and rlist. It turns out that I made a silly mistake. I checked the mdout.mdp rather than the mg.log file for rlist value. According to mg.log file, Gromacs set rlist = 1.47, which is just 0.7 larger than rvdw = 1.4. Is this possible to cause any accuracy problems for LJ energy?

> 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

I use GROMOS 54a7 force field. In the paper defining this ff, I only found the method and parameters used to calculate coulomb force, but did not see those for van der waals force.  Therefore, I randomly chose vdwtype = cut-off and vdw-modifier = force switch. Can you give me some guidance about which method and parameters used to calculate the vdw interaction are more suitable for GROMOS 54a7 ff?

--

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

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

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

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