Hello All,
I am looking for a very simple (step-by-step) tutorial on AFM pulling
simulations (constant force/ constant velocity) with gromacs.
Can someone point me to a simple tutorial to perform these simulations with
gromacs?
Thanks,
--
X Rules wrote:
Hello All,
I am looking for a very simple (step-by-step) tutorial on AFM pulling
simulations (constant force/ constant velocity) with gromacs.
Can someone point me to a simple tutorial to perform these simulations
with gromacs?
Thanks,
http://www.gromacs.org/Documentation/Tutorials
On 03/22/2011 11:02 AM, X Rules wrote:
Hello All,
I am looking for a very simple (step-by-step) tutorial on AFM pulling
simulations (constant force/ constant velocity) with gromacs.
Can someone point me to a simple tutorial to perform these
apply the
force in that direction).
Date: Tue, 22 Mar 2011 11:15:54 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] AFM pulling simulations
X Rules wrote:
Hello All,
I am looking for a very simple (step-by-step) tutorial on AFM pulling
simulations
too eager to send an email..
I think playing with editconf with princ flag should do the trick ..
sorry folks and thanks for the help !!
From: xru...@live.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] AFM pulling simulations
Date: Tue, 22 Mar 2011 15:47:41 +
Thanks
On 26/08/10 19:56, chris.ne...@utoronto.ca wrote:
Natalie:
It would also be a good idea for you to ensure that your supervisor
knows how difficult it is to learn and correctly apply these methods. If
they think that a person can learn linux and gromacs and the gromacs
pull code in a short
Hi,
I'm a complete novice when it comes to using any kind of command
prompt based programmes and hadn't even heard of Linux until my
supervisor wanted me to use gromacs ... so needless to say I'm running
into a few problems!!
I've managed to perform all the generic energy minimisations
Natalie Stephenson wrote:
Hi,
I'm a complete novice when it comes to using any kind of command prompt
based programmes and hadn't even heard of Linux until my supervisor
wanted me to use gromacs ... so needless to say I'm running into a few
problems!!
I've managed to perform all the
Quoting Justin A. Lemkul jalem...@vt.edu:
Natalie Stephenson wrote:
Hi,
I'm a complete novice when it comes to using any kind of command
prompt based programmes and hadn't even heard of Linux until my
supervisor wanted me to use gromacs ... so needless to say I'm
running into a few
Natalie:
It would also be a good idea for you to ensure that your supervisor
knows how difficult it is to learn and correctly apply these methods.
If they think that a person can learn linux and gromacs and the
gromacs pull code in a short period of time, then the stage is set for
Hi,
The unit of the afm_rate in the GROMACS manual 3.3-1 is nm/ps.
I have read something in an earlier thread on this list that this might
be a typo, it should be nm/timestep. Does anyone know? I would be happy
if I could have that information.
Moreover, I am a bit confused about the output
completely rewritten the pull code.
There are separate xvg output files with only the positions and only the forces.
Berk.
Date: Thu, 14 Aug 2008 08:30:35 +0200
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] AFM pulling rate
Hi,
The unit of the afm_rate
Dear all,
I simulate pulling experiment with the AFM-option in GROMACS. I
calculate the forces from the .pdo file:
F = k_c (/spr/ - /pullg/)
with F the force, k_c the springconstant. spring is the position of the
spring and /pullg/ the position of the pullgroup. after the
bond-breakage the forces
Dear all,
I simulate pulling experiment with the AFM-option in GROMACS. I
calculate the forces from the .pdo file:
F = k_c (/spr/ - /pullg/)
with F the force, k_c the springconstant. spring is the position of the
spring and /pullg/ the position of the pullgroup. after the
bond-breakage the forces
Hello,
I am attempting to use AFM pulling on a 17 amino acid peptide, but am having
trouble with the 'group' concept. I've read the manual and searched sample
XXX.ndx files, but have had no luck. How would I define the first amino acid
as the reference group (i.e. - fixed in space) and the last
From: Zhou Bo [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] AFM Pulling and com motion
Date: Fri, 21 Sep 2007 00:49:21 +0800
Thanks for your reply. There is no absolute reference here. The system
From: Zhou Bo [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
To: gmx-users@gromacs.org
Subject: [gmx-users] AFM Pulling and com motion
Date: Thu, 20 Sep 2007 11:06:09 +0800
Hi GXM Users,
I'm trying to execute some AFM Pulling. I followed the pull
Thanks to Berk. I just tested two system, one with stopcm and the other
without stopcm. I calculated the pull forces and compared them with each
other. There are really some distinct differences between them during the
80ps simulation. I worry about it, for example, in long time simulations, so
You didn't tell if you are using an absolute reference or not.
With an absolute reference you should not remove the com motion.
Berk.
From: Zhou Bo [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] AFM
for GROMACS users gmx-users@gromacs.org
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] AFM Pulling and com motion
Date: Thu, 20 Sep 2007 22:44:29 +0800
Thanks to Berk. I just tested two system, one with stopcm and the other
without stopcm. I calculated the pull forces and compared them with each
Hi GXM Users,
I'm trying to execute some AFM Pulling. I followed the pull code tutorial
from GMX WORKSHOP 2007, and I found there is no specific to com motion in
mdp, so the default is comm-mode=Linear and comm-grps=System. I was
confused about it as I believed we should not stopcm when
Hi
GXM Users,
I'm trying to execute some AFM pulling. My index file contains two
groups, [TopPeptide] and [DMPC]. I execute grompp, then when I try
to execute mdrun:
[EMAIL PROTECTED] SteeredMD]$ mdrun -s SMD-01.tpr -o SMD-01 -c
AfterSMD-01 -e SMD-01 -g SMD-01 -pi PeptidePull.ppa
Hi all, nevermind, I caught my own mistake. (I hope this might be
useful for someone in the future).
PeptidePull.ppa is my input file, specifying the parameters for my
pulling.
-po PeptidePull is the output file. The problem here is that I used the
same name.
When it crossed over to
From: Susanna Hug [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
To: gmx-users@gromacs.org
Subject: [gmx-users] AFM pulling
Date: Mon, 14 Aug 2006 13:23:28 +0200
Hi gmx-users!
I am trying to simulate the diffusion of mannitol through a lipid bilayer
Thanks, that's good to know!
Susanna
From: Susanna Hug [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
To: gmx-users@gromacs.org
Subject: [gmx-users] AFM pulling
Date: Mon, 14 Aug 2006 13:23:28 +0200
Hi gmx-users!
I am trying to simulate
Hello Bob,
have you tried to define the initial position of the AFM-tip? It needs
to be set to the position of the COM of the group you want to pull. try
and add
afm_init1 = x y z
(x y z = position where the afm should be) to your pull.ppa.
Otherwise your afmspring is extended from the
Hello everyone,
I am using AFM pulling to drag a dna base across the surface of a graphene. I'm
doing this in vaccuum. It seems that the base is pulled at the same rate no
matter what value I specify in afm_rate1. Here is my pull.ppa file:
runtype = afm
group_1 = ssdna-ions
pulldim = N N Y
Hi again,
I pretty much went about the setting up of afm pulling calculations.
Still I am a little bit concern about the results. When using gmx3.2.1
and applying a Linear removal of the center of mass (i.e. translation) I
see the cell unit still moving during the simulation in a direction
Hi
There seems to be something wrong with your init-vector.
Ich have written a small python script, which simply calculates the
vector for convenience purposes. You still need the pull- and COM-group
coordinates, though. But that shouldn't be a problem.
If you want it, I'll send it via mail.
Thanks Emily and Maik for your feed-back
You both are right regarding the init vector. I happened to be the sign
of it as Emily guessed. Changing the direction by doing xpull-xref,
ypull -yref, zpull-zref and not xref-xpull.works fine. Thanks for
the offer on the script though.
Thanks
Emily Walton wrote:
afm_init describes only the initial position of the spring. afm_dir
describes how that position will change with time. You can normalize
afm_init and use it for afm_dir if you want- you'd be pulling along
the direction connecting the com of your reference and pull
Dear all,
I am simulating an unbinding process with the pull code (afm option).
I've been reading previous posts about this option and I just wanted to
clarify some ideas and ask some questions. There are:
1-The pulling can be done choosing two different molecules. Why a
particular group within
Hi,
Dear all,
I am simulating an unbinding process with the pull code (afm option).
I've been reading previous posts about this option and I just
wanted to
clarify some ideas and ask some questions. There are:
1-The pulling can be done choosing two different molecules. Why a
particular group
Hi all,
I am a bit confused about some points on the manual (section 6.1, manual
3.2). I f i define two groups: one that will be pulled and the other as
reference group; then the force constant and the rate, must i define also
the afm_dir and the afm_unit? In my mind, if i define two groups
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