Hi everyone!
I want to add the distance restraint for some atom pairs. However, it is not
working at all. The yielded bond length can easily go beyond 0.5~0.6 nm. Has
anyone got a hint? Thanks very much!
[ distance_restraints]
; ai aj type index type' low up1 up2 fac
157910
On 9/27/12 12:04 PM, Paula Andrea Delgado Pinzon wrote:
Hello gromacs users,
I am doing energy minimization of a big protein with distance restraint (i need
to create interactions between a group of residues, so i need them to be
close), but in the resultant pdb a don't see those residues cl
Hello gromacs users,
I am doing energy minimization of a big protein with distance restraint (i need
to create interactions between a group of residues, so i need them to be
close), but in the resultant pdb a don't see those residues close, so how can I
verify that the distance restraint are wo
ikhil
*From:* nikhil damle
*To:* jalem...@vt.edu; Discussion list for GROMACS users
*Sent:* Mon, 8 February, 2010 10:14:10 AM
*Subject:* Re: [gmx-users] Distance restraint energy terms
I have already included the [distance_restraints] section in .top file.
In principl
equal for both
pairs.
Am I understanding correctly ?
Regards,
Nikhil
From: nikhil damle
To: jalem...@vt.edu; Discussion list for GROMACS users
Sent: Mon, 8 February, 2010 10:14:10 AM
Subject: Re: [gmx-users] Distance restraint energy terms
I have already
constant to be
1000 even though fac coloumn > 1. I wish to restrain the distance between on
two atoms.
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Sat, 6 February, 2010 6:10:12 PM
Subject: Re: [gmx-users] Distance restraint energy te
nikhil damle wrote:
Hi,
I have applied distance restraints on my system during MD simulation
through following options:
"disre = simple" and disre_fc = 2000 in .mdp file.
Now i wish to see the energy term corresponding to these restraints in
principle to be written in .edr file. But g_energ
Hi,
I have applied distance restraints on my system during MD simulation through
following options:
"disre = simple" and disre_fc = 2000 in .mdp file.
Now i wish to see the energy term corresponding to these restraints in
principle to be written in .edr file. But g_energy programme does not list
On 1/7/10 3:48 PM, Feng Xu wrote:
Hi, Justin, Thank you for your answer to my previous post. I just turned
on the mail delivery from this list,
so I reply you here, hope it is not so disruptive to this thread.
My problem for the previous post is resolved, the problem is I should
have modified
Hi, Justin, Thank you for your answer to my previous post. I just turned on
the mail delivery from this list,
so I reply you here, hope it is not so disruptive to this thread.
My problem for the previous post is resolved, the problem is I should have
modified files in ~username/gromacs/.., instead
On 1/7/10 2:58 PM, Hans HEINDL wrote:
interstingly the distance restrain works well when one chooses the bond
type 2 whatever this means physically
[bonds]
.
.
.
.
.
.
1 614 2 5,761 40
What you've specified is not a distance restraint, it is just a bond. Bond
types a
interstingly the distance restrain works well when one chooses the bond
type 2 whatever this means physically
[bonds]
.
.
.
.
.
.
1 614 2 5,761 40
Hans
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the
Mark Abraham escreveu:
Alexandre Suman de Araujo wrote:
Hi Gmxers
Some months ago I performed some simulations, with GMX 3.3.3 version,
where I apply distance restraint between water oxygen atoms and a
static dummy site located at the center of a sphere to keep waters
inside this sphere. Aft
Alexandre Suman de Araujo wrote:
Hi Gmxers
Some months ago I performed some simulations, with GMX 3.3.3 version,
where I apply distance restraint between water oxygen atoms and a static
dummy site located at the center of a sphere to keep waters inside this
sphere. After performed an upgrade
Hi Gmxers
Some months ago I performed some simulations, with GMX 3.3.3 version,
where I apply distance restraint between water oxygen atoms and a static
dummy site located at the center of a sphere to keep waters inside this
sphere. After performed an upgrade to GMX 4.0.5 version this distance
Hi,
My apologies in advance, I'm aware that this is probably a stupid question...
If I've run a simulation using the umbrella sampling branch of the pull code (gromacs 3.3.1), in which I restrain a small molecule to a membrane, which options must I include when running g_energy to obtain the energy
Pathumwadee Intharathep wrote:
Dear gmx's user,
May I asked you some technicl Questions?
Do you know how to make distance restraint in gromacs?
what I did I have created file name "disre.itp" as shown below
[ distance_restraints ]
; aiaj type index type low up1 up2 fac
489 1133 1
Dear gmx's user,
May I asked you some technicl Questions?
Do you know how to make distance restraint in gromacs?
what I did I have created file name "disre.itp" as shown below
[ distance_restraints ]
; ai aj type index type low up1 up2 fac
489 1133 1 1 1 0.25 0.35 0.40 1.0
Hi,
I have a system with a protein and two different ligands.
I'm trying to use distance restrain to hold the ligands inside the
protein during a free energy calculation.
If I use the distance restrains only between the protein and the first
ligand I don't get any error, but if I introduce restrai
19 matches
Mail list logo
