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 <jalem...@vt.edu>
*To:* Golshan Hejazi <golshan.hej...@yahoo.com>; Discussion list for GROMACS
users <gmx-users@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
jalem...@outerbanks.umaryland.edu <mailto:jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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