[gmx-users] Bond energy doesn't appear in gromacs rerun

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 8/7/13 2:26 PM, Golshan Hejazi wrote:
> sorry yes I do use:
>
> ; Constraints bonds
> constraints              = all-bonds
> constraint_algorithm     = lincs
> lincs-order              = 4
> lincs-warnangle          = 30
> user1-grps               = System
>
> But what does it mean?
>
>

That means your bond lengths are fixed.  Thus, there can be no energy term 
associated with them.  See the LINCS paper for details.

-Justin

> --------------------------------------------------------------------------------
> *From:* Justin Lemkul <jalemkul at vt.edu>
> *To:* Golshan Hejazi <golshan.hejazi at yahoo.com>; Discussion list for GROMACS
> users <gmx-users at gromacs.org>
> *Sent:* Wednesday, August 7, 2013 2:11 PM
> *Subject:* Re: [gmx-users] Bond energy doesn't appear in gromacs rerun
>
>
>
> On 8/7/13 2:09 PM, Golshan Hejazi wrote:
>  > Hello everyone,
>  >
>  > I am doing single point energy calculation for a certain configuration of a
> molecule using rerun option of gromacs. But in the energy output, there is no
> Energy term related to BOND.
>  >
>  > Do you know why?
>  >
>
> Are you using constraints?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
>
> ==================================================
>
>

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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