http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html?highlight=pairs%20
with particular attention to values of gen-pairs, nrexcl, [pairs].
Best regards
Alessandra
On Thu, Feb 13, 2020 at 9:49 AM Luirink, R.A. wrote:
&g
Anyone has advice/feedback?
On 06/02/2020, 16:55, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Luirink, R.A." wrote:
Here some output to illustrate what I mean. This is what you would expect
and what I also get for standard atom-atom interactions, not 1
(kJ/mol)
LJ-14:CXZ-CXD 0.186637 0.16 0.5077671.03044 (kJ/mol)
It seems like a bug to me, or I have overlooked something..
On 06/02/2020, 14:44, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Luirink, R.A." wrote:
Gromacs version
Gromacs version 2018.6 btw.
On 06/02/2020, 13:54, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Luirink, R.A." wrote:
What I have tried is, instead of adding them to the [ pairs ] block, is
change the epsilon value manually via the [ nonbon_params ] block.
way to do so).
From: "Luirink, R.A."
Date: Thursday, 6 February 2020 at 11:49
To: "gmx-us...@gromacs.org"
Subject: specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output
Hello,
I try to specify a pair of atoms to be treated as a 1-4 interaction (I replaced
Hello,
I try to specify a pair of atoms to be treated as a 1-4 interaction (I replaced
a covalent bond to a soft core restraint for free energy calculation purposes,
and now gromacs does not recognize it anymore as 1-4 interaction, but it should
still be treated as such).
I added the pair to the
ot; wrote:
On 12/13/19 9:43 AM, Luirink, R.A. wrote:
> I found the solution!
Please post the solution so that others can benefit in the future.
-Justin
>
> On 13/12/2019, 13:53, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf
I found the solution!
On 13/12/2019, 13:53, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Luirink, R.A." wrote:
Hi,
I would like to constrain a bond between two dummy atoms using LINCS
constraints. As I want to perturb the atoms towards a N-H bond, I wou
Hi,
I would like to constrain a bond between two dummy atoms using LINCS
constraints. As I want to perturb the atoms towards a N-H bond, I would like to
pre-treat it as such, due to the low mass of one of the dummy atoms.
Is this possible somehow? And, if not, how is the constraint introduced dur
