On 6/29/12 9:03 AM, Raj wrote:
HI , I have been performing SMD after reading bevan lab tutorial. The
tutorial was very informative in basic aspects. Now I have my ligand inside
the protein and I wan to pull it out in a specific direction. I applied
force separately along the X, Y and Z axis . I
HI , I have been performing SMD after reading bevan lab tutorial. The
tutorial was very informative in basic aspects. Now I have my ligand inside
the protein and I wan to pull it out in a specific direction. I applied
force separately along the X, Y and Z axis . In which none of the pull seems
to b
---
Message: 4
Date: Wed, 15 Dec 2010 11:04:12 -0500
From: chris.neale at utoronto.ca
Subject: [gmx-users] Com Pulling
To: gmx-users at gromacs.org
Message-ID: <20101215110412.imqto29twk8ksk80 at webmail.utoronto.ca>
Content-Type: text/plain;charset=ISO-8859-1;DelSp="
If I understand correctly, you want to apply a biasing force and you
also want to have an "unbiased" simulation. These two things are not
possible in combination. There are a variety of techniques available
that will give you particular information. For example, you can
extract the unbiased
C Johnson wrote:
If you're proceeding blindly, then you're likely going to frustrate yourself to
no end. There is literature relevant to what you're doing - pulling on
peptides/proteins to unfold them is something that's been done. So you should
have some methodological precedent.
"Non-Pr
>If you're proceeding blindly, then you're likely going to frustrate yourself
>to
>no end. There is literature relevant to what you're doing - pulling on
>peptides/proteins to unfold them is something that's been done. So you should
>have some methodological precedent.
>"Non-Protein" is a d
C Johnson wrote:
Hi all,
I'm trying to do some pulling on the speptide.pdb file given in the tutor.
I first ran pdb2gmx:
>>> pdb2gmx -f speptide.pdb -p speptide.top -o speptide.gro
Then did editconf to put speptide at the bottom (y-axis) center of a
longer box:
>>> editconf -f speptid
Dear Joe,
check your fatal error message, it may have a typo in the work
"goups", but it does outline your problem fairly completely. That
said, you did a 99th percentile job in posting your inputs and
outputs, making it easy for us to help.
quoting your post:
Group Non-Protein not found
Hi all,
I'm trying to do some pulling on the speptide.pdb file given in the tutor.
I first ran pdb2gmx:
>>> pdb2gmx -f speptide.pdb -p speptide.top -o speptide.gro
Then did editconf to put speptide at the bottom (y-axis) center of a longer box:
>>> editconf -f speptide.gro -o newbox.gro -cen
Warren,
You're right that one can not use constraints if they are also using lincs on
C-C bonds.
However, constraining this bond is not necessary with a 1 fs timestep.
Even while constraining C-C bond lengths, one can still use harmonic restraints
instead (also from the pull code).
Before get
Maybe I'm confused here, but the manual says that the pull code will not in
general work for groups that have other constraints.
To quote the last part of section 6.3:
There is one important limitation: strictly speaking, constraint forces can
only be calculated between
groups that are not conn
yes. use the pull code. check your convergence carefully.
--original message --
Hi All,
I was wondering if it is possible to pull on a single chain? I would
like to anchor the C-terminus and pull the N-terminus and have a plot
of pulling force vs displacement.
I'm looking for more or les
Hi All,
I was wondering if it is possible to pull on a single chain? I would like to
anchor the C-terminus and pull the N-terminus and have a plot of pulling force
vs displacement.
I'm looking for more or less a yes or no answer, if you would like to elaborate
then I won't complain :)
Thank
Hi,
I've been working a time ago with Pull code in Gromacs 3.3.1, calculating the
components of the applied force from pull.pdo file.
Now, using 4.0.5 version and re-starting with COM Pulling, as well as the
great optimization, I've found that the outputs show something like the
modulus
o
Try changing
pull_dim = N N Y
to
pull_dim = Y Y Y
And check the manual for what it does.
Note that some of your other pull options are irrelevant tot he type
of sampling that you appear to be doing, but that should not matter.
Chris.
-- original message --
I have a results of my MD and
Hi all !
I have a results of my MD and i have found a water molecule that was getting
closer to my substrate on one frame of my dynamic. The distance is 3.4 A.
Now I have to immobillize this water on this distance during the next step
of MD by using a harmonic potential as the distance constraint,
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