Sorry forgot to write the subject in previous mail.
Dear gmx-users,
We intend to perform free energy calculations by pulling a polypeptide
along water-hexane interface. We need to pull the polypypeptide from the
water layer towards the hexane layer (crossing the interface). For this we
position r
Dear users,
I have a sytem including protein, lipids, and water. My protein is in
center of the box. Now i want it stays at one side of the box. Which tool
or command should i use to pull the protein to a any mong muốn location ?
Thankful for any help !
Thu
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On 5/29/13 9:19 AM, Sathish Kumar wrote:
Dear Sir,
In pulling simulations how to set pull_rate and
pull_k .On which basis we can set these values.
There is no systematic way to set these values, at least none that I know of.
Everyone has their own impression of wha
The force should not probably exceed kT product too much...
Dr. Vitaly Chaban
On Wed, May 29, 2013 at 3:19 PM, Sathish Kumar wrote:
> Dear Sir,
> In pulling simulations how to set pull_rate and
> pull_k .On which basis we can set these values.
> --
> regards
> M.Sathish
Dear Sir,
In pulling simulations how to set pull_rate and
pull_k .On which basis we can set these values.
--
regards
M.SathishKumar
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* Please search the archive at
http:
Sir,
I want to do pulling simulations for membrane protein and gold
nanoparticles. Can you please suggest me some tutorials.
Thank You
--
regards
M.SathishKumar
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* Pl
I came across one such application name PLUMED plugin for gromacs, for
dihedral restraints as the reaction coordinate.
If you can suggest any other application for the same, kindly let me know.
--Thanks
Neeru
> On 4/15/13 2:27 AM, neeru sharma wrote:
> > Dear gromacs users,
> >
> >
> > I want t
On 4/15/13 2:27 AM, neeru sharma wrote:
Dear gromacs users,
I want to calculate PMF using pull code in gromacs, taking a psi angle as
the reaction coordinate.
I have a doubt where it is possible with the geometry options, currently
available in gromacs?
This is an application of either dih
Dear gromacs users,
I want to calculate PMF using pull code in gromacs, taking a psi angle as
the reaction coordinate.
I have a doubt where it is possible with the geometry options, currently
available in gromacs?
Thanks and regards
Neeru
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http
On 4/14/13 2:09 AM, Kshatresh Dutta Dubey wrote:
Dear Users,
I am using umbrella sampling method for unwinding of a peptide from binding
site. I have to pull peptide in -X (negative direction). Can anyone suggest me
keyword for this purpose. Should I use pulling_dim = Y N N or have to define
Dear Users,
I am using umbrella sampling method for unwinding of a peptide from binding
site. I have to pull peptide in -X (negative direction). Can anyone suggest me
keyword for this purpose. Should I use pulling_dim = Y N N or have to define
some other keywords.
I will be thankful for every
On 2/8/13 6:00 AM, Steinbrecher, Thomas (IBG) wrote:
Dear Gromacs users,
I encountered two problems in using g_wham to calculate pmf curves from a
pulling simulation. My system consists of a water molecule which is pulled
through a bilayer (the reference group). I used gromacs 4.5.6 with the
Dear Gromacs users,
I encountered two problems in using g_wham to calculate pmf curves from a
pulling simulation. My system consists of a water molecule which is pulled
through a bilayer (the reference group). I used gromacs 4.5.6 with the
following pull code options:
pull= umbrell
On 12/10/12 10:50 AM, Steven Neumann wrote:
Would you also specify in each US window specific residue instead of
the whole protein?
That really depends on whether the residue-ion distance reflects the desired
reaction coordinate and if doing so is superior to using the protein-ion
distance
Would you also specify in each US window specific residue instead of
the whole protein?
Sreven
On Mon, Dec 10, 2012 at 2:47 PM, Steven Neumann wrote:
> On Mon, Dec 10, 2012 at 2:11 PM, Justin Lemkul wrote:
>>
>>
>> On 12/10/12 9:01 AM, Steven Neumann wrote:
>>>
>>> Dear Gmx Users,
>>>
>>> I am
On Mon, Dec 10, 2012 at 2:11 PM, Justin Lemkul wrote:
>
>
> On 12/10/12 9:01 AM, Steven Neumann wrote:
>>
>> Dear Gmx Users,
>>
>> I am pulling away cation from the protein glutamic acid residue with:
>>
>> pull= umbrella
>> pull_geometry = distance ; simple distance increase
>> pul
On 12/10/12 9:01 AM, Steven Neumann wrote:
Dear Gmx Users,
I am pulling away cation from the protein glutamic acid residue with:
pull= umbrella
pull_geometry = distance ; simple distance increase
pull_dim= N N Y
pull_start = yes ; define initial COM distance
As a side note:
The rupture process is a stochastic process, so a single rupture force
is meaningless, since it is a distributed property. So you need to do
many simulations to get the distribution / average rupture force.
It that same like equilibrium properties, one doesn't determine them
fr
Thank you Justin.
On Wed, Jun 27, 2012 at 2:39 PM, Justin A. Lemkul wrote:
>
>
> On 6/27/12 9:36 AM, Steven Neumann wrote:
>>
>> On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul wrote:
>>>
>>>
>>>
>>> On 6/27/12 7:48 AM, Steven Neumann wrote:
Dear Gmx Users,
I obtained
On 6/27/12 9:36 AM, Steven Neumann wrote:
On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul wrote:
On 6/27/12 7:48 AM, Steven Neumann wrote:
Dear Gmx Users,
I obtained a protein-ligand complex from 100ns simulation. Now I am
pulling my ligand away from the protein after the energy minimz
On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul wrote:
>
>
> On 6/27/12 7:48 AM, Steven Neumann wrote:
>>
>> Dear Gmx Users,
>>
>> I obtained a protein-ligand complex from 100ns simulation. Now I am
>> pulling my ligand away from the protein after the energy minimzation
>> in water and equilibra
On 6/27/12 7:48 AM, Steven Neumann wrote:
Dear Gmx Users,
I obtained a protein-ligand complex from 100ns simulation. Now I am
pulling my ligand away from the protein after the energy minimzation
in water and equilibration of 100ps (two coupling baths: Protein,
LIG_Water_and_ions).
Then I proce
Dear Gmx Users,
I obtained a protein-ligand complex from 100ns simulation. Now I am
pulling my ligand away from the protein after the energy minimzation
in water and equilibration of 100ps (two coupling baths: Protein,
LIG_Water_and_ions).
Then I proceed my pulling :
grompp -f pull.mdp -c npt.gro
On 8/06/2012 8:35 PM, Steven Neumann wrote:
Dear Gmx Users,
I pulled my ligand away from the protein and I found out that after
getting rid of PBC (trjconv -pbc whole)
There is no magic way to "get rid of PBC", and "-pbc whole" is certainly
not it. Read trjconv -h and see
http://www.gromacs
Dear Gmx Users,
I pulled my ligand away from the protein and I found out that after getting
rid of PBC (trjconv -pbc whole) my ligand goes outside the box? Is it fine
or should I increase my box as I want to run umbrella sampling?
Thanks,
Steven
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Wright, Louise wrote:
Hi Justin,
thanks for your reply. Yes the distances get a lot larger and are
definitely not just fluctuating. It is hard to demonstrate this without
showing you the whole file which is huge. However, I have used the same
input files with gromacs 4.5.4 just now and it
Hi Justin,
thanks for your reply. Yes the distances get a lot larger and are definitely
not just fluctuating. It is hard to demonstrate this without showing you the
whole file which is huge. However, I have used the same input files with
gromacs 4.5.4 just now and it works- I think it might b
Wright, Louise wrote:
Hi
I am trying to use the pull code of gromacs (version 4.5.5) to constrain
the com of a number of groups (labelled CIT, CIT1, CIT2...) to a
reference group (labelled GOLD). This is the segment of the .mdp file I
have used:
;CoM pull calculations
pull
Hi
I am trying to use the pull code of gromacs (version 4.5.5) to constrain the
com of a number of groups (labelled CIT, CIT1, CIT2...) to a reference group
(labelled GOLD). This is the segment of the .mdp file I have used:
;CoM pull calculations
pull= constraint
pull_geomet
2011 09:34:02 -0500
>>From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
>>
>>Subject: Re: [gmx-users] pulling force vs free energy
>>To: Discussion list for GROMACS users ><mailto:gmx-users@gromacs.org>**>
>>
Vijayaraj wrote:
Message: 4
Date: Wed, 16 Nov 2011 09:34:02 -0500
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] pulling force vs free energy
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Mess
>
> Message: 4
> Date: Wed, 16 Nov 2011 09:34:02 -0500
> From: "Justin A. Lemkul"
> Subject: Re: [gmx-users] pulling force vs free energy
> To: Discussion list for GROMACS users
> Message-ID: <4ec3c9da.7040...@vt.edu>
> Content-Type: text/
Vijayaraj wrote:
Hi,
What is the relation between pulling force and free energy of binding.
can we relate the maximum pulling force with the free energy. for
example, 2 systems has the maximum pulling force and free energy as
below from umbrella sampling and g_wham analysis,
Hi,
What is the relation between pulling force and free energy of binding. can
we relate the maximum pulling force with the free energy. for example, 2
systems has the maximum pulling force and free energy as below from
umbrella sampling and g_wham analysis,
max. force
Dear Adam:
I have a number of questions listed below. But first, I think it would
be useful if you explain exactly what you want to accomplish and how
you tried to do this with non-modified code and what problem you ran
into that caused you to modify the code. After you outline that,
plea
Hi all,
I am trying to measure the energy curve of unwinding the SNARE protein
complex. This requires pulling the C-termini of two helices apart from each
other, while fixing certain other parts of the complex. To do this I
excluded the reference group, so that all groups were pulled to absolute
Thanks for you prompt reply - I'll try that and post back.
-SA
On Tue, May 31, 2011 at 4:46 PM, Justin A. Lemkul wrote:
>
>
> Shay Teaching wrote:
>
>> Dear gromacs users,
>>
>> I am trying to pull a ligand out of a cavity of a membrane protein (along
>> the Z axis).
>> Problem is, that with eve
Shay Teaching wrote:
Dear gromacs users,
I am trying to pull a ligand out of a cavity of a membrane protein
(along the Z axis).
Problem is, that with every pull settings I have tried the ligand gets
"stuck" on the protein's center of mass. How can I make it go all the
was to the bulk water?
Dear gromacs users,
I am trying to pull a ligand out of a cavity of a membrane protein (along
the Z axis).
Problem is, that with every pull settings I have tried the ligand gets
"stuck" on the protein's center of mass. How can I make it go all the was to
the bulk water?
It always gets stuck on the
Jon Mujika wrote:
Dear all,
I am trying to pull a metal out of the protein binding pocket following
a cavity in the protein structure. I followed the tutorial, but I find
few problems:
1) When the metal leaves the binding pocket, some ligands "follow" the
metal, even that I restrained th
Dear all,
I am trying to pull a metal out of the protein binding pocket following a
cavity in the protein structure. I followed the tutorial, but I find few
problems:
1) When the metal leaves the binding pocket, some ligands "follow" the
metal, even that I restrained the position of protein atom
Thank you again for your reply
On Wed, Mar 16, 2011 at 7:35 PM, wrote:
> 2-When you limit your sampling phase space,it can make some Errors,
>> Because you may ignore some important regions(where you don't know them
>> and you can't predict there).
>>
>
> I agree with the idea that underlies you
2-When you limit your sampling phase space,it can make some Errors,
Because you may ignore some important regions(where you don't know
them and you can't predict there).
I agree with the idea that underlies your point, but it is not a
problem. You don't need to sample all intervening phase s
Dear Chris
Thanks for your reply
2-When you limit your sampling phase space,it can make some Errors,Because
you may ignore
some important regions(where you don't know them and you can't predict
there).
In the other hands,When we pull drug along a line,although we had not
restrain it, but in fact t
1. yes. it is acceptable. It is different, but neither method is de
facto better.
2. to enhance convergence by limiting the amount of phase space that
must be sampled. Changing the restraints can change the profile, but
if you care only about the integrated standard binding free energy
th
Dear All
Afew question about Pulling in Umberella Sampling
1-the goal of pulling is making some primary structures (in different
distances) to do umberella sampling for each one of them.
I can make these states by transporting my ligands along a vector to
prepare these primary structures.Is this
mohsen ramezanpour wrote:
Dear All
I am using this configuration.mdp file for pulling.this is the same as
umbrella sampling,of course I have changed some parts of it
according to my problem(protein-ligand free energy).but when i use
grompp this warning is occuring.
The only reason I can see
Dear All
I am using this configuration.mdp file for pulling.this is the same as
umbrella sampling,of course I have changed some parts of it
according to my problem(protein-ligand free energy).but when i use grompp
this warning is occuring.
WARNING 1 [file configuration.mdp, line unknown]:
Unknown
Dear All
I want to pull my ligand from protein which is docked to it for generating
configurations for umbrella sampling.
But my ligand is located in a hole inside of protein.
If I pull it along the line which is connecting COMs of them,the ligand may
be arrested(constraint)inside of hole.
Am I for
Natalie Stephenson wrote:
Hi ...
Just wondering if there's a way, during pulling simulations, to
immobilise say the C-terminus of the protein.
I've been running through the 'Umbrella Sampling' tutorial with my own
protein. Within this tutorial the ChainB is used as the immobile
referenc
Hi ...
Just wondering if there's a way, during pulling simulations, to immobilise say
the C-terminus of the protein.
I've been running through the 'Umbrella Sampling' tutorial with my own protein.
Within this tutorial the ChainB is used as the immobile reference - so it is
this that is posit
Xiaohua Zhang wrote:
Sorry for my mistake about the group names.
I was confused just to find it difficult to simultaneously fix one group
(layer0) but pull another (layer2). It is possible to fix an absolute
reference and pull layer2, but layer0 might follow the motion of layer2.
For such e
Xiaohua Zhang wrote:
Dear gmx-users
I want to design such kind of computer experiment:
For a system composed of non-bonded three layers (carbon nanotubes,
graphene, or whatever), I want to fix layer0 (the group name) to exactly
(0,0,0), and pull layer2 by a constant force, for example, alon
Sorry for my mistake about the group names.
I was confused just to find it difficult to simultaneously fix one group
(layer0) but pull another (layer2). It is possible to fix an absolute
reference and pull layer2, but layer0 might follow the motion of layer2. For
such experiment, the relative spee
Dear gmx-users
I want to design such kind of computer experiment:
For a system composed of non-bonded three layers (carbon nanotubes,
graphene, or whatever), I want to fix layer0 (the group name) to exactly
(0,0,0), and pull layer2 by a constant force, for example, along positive x
all the time.
abdul wadood wrote:
Dear GMX user
I am working on enzyme ligand complex and want to calculate pmf of the
complex.
I have successfully energy minimized and equilibrated the system.
But when I pull the ligand from the complex using the md_pull.mdp file
then instead of ligand the protein is com
Dear GMX user
I am working on enzyme ligand complex and want to calculate pmf of the complex.
I have successfully energy minimized and equilibrated the system.
But when I pull the ligand from the complex using the md_pull.mdp file then
instead of ligand the protein is come out of the system.
I ha
Hi all,
Can anyone please give me a mdp file for running pulling simulations
in implicit solvent using GROMACS?
Thanks in advance
Samrat
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Please search the archive at http://www
Sorry, I want to ask the same question I had a week ago. I need your advice
in COM PULL.
This is a part of article which describes methodology "...with respect to
the atomic distance between the carbonyl carbon of the substrate and the
oxygen atom of the identified nucleophilic water, a constraine
Sorry for so disordered questions...
<3. use the pull code. I don't know exactly what you want to do
here...perhaps harmonically restrain the distance between the two mentioned
groups to some specified value? No need to rename the water, just make an
index group.>
The problem is that I don't know
Алексей Раевский wrote:
Sorry for so disordered questions...
<3. use the pull code. I don't know exactly what you want to do
here...perhaps harmonically restrain the distance between the two
mentioned groups to some specified value? No need to rename the water,
just make an index group.>
Sorry for so disordered questions...
<3. use the pull code. I don't know exactly what you want to do
here...perhaps harmonically restrain the distance between the two mentioned
groups to some specified value? No need to rename the water, just make an
index group.>
The problem is that I don't know
Sorry for so disordered questions...
<3. use the pull code. I don't know exactly what you want to do
here...perhaps harmonically restrain the distance between the two mentioned
groups to some specified value? No need to rename the water, just make an
index group.>
The problem is that I don't know
First let me mention that I only scanned the mammoth manuscript
snippet. Nevertheless, I'll try to address your questions.
1. You are physically able to use spc in place of tip3p. Whether or
not that is a good idea is up to you to decide. Read the literature
including the spc, tip3p, and ot
Hi all.
I have to reproduce an experiment from the article "Identification of the
nucleophilic factors and the productive complex for the editing reaction by
leucyl-tRNA synthetase" (by Yohsuke Hagiwara a,b, Osamu Nureki c, Masaru
Tateno a,b,*). This is one of the steps of education I have to comp
Hey,
has anyone actually succeeded doing pulling with gromacs 4.0.5 keeping
the distance between
a froozen and a non froozen group (so not pulling into a direction but
just applying the harmonic potential to the distance).
If so, could you send me the mdp file showing how you set up the whole
thin
Hi again,
I actually figured it out. Turns out, it was a stupid formatting error in
the .mdp file. Even though I had it as shown, it didn't read the pull
command because it wasn't formatted properly (thought it was still a part
of the first line). Sorry guys.
--Johnny
> Hi Justin,
>
> Thx for th
Hi Justin,
Thx for the reply. By pull apart, I just wanted to expose an 'activation
site' by using a force. It is somewhat similar to pulling two domains of a
protein away from each other. I'm not aiming to undo any secondary
structure. I hope this is clearer. Thanks again!
--Johnny
>
>
> Johnn
Johnny Lam wrote:
Hi again,
I am trying to pull apart a CG protein (to verify CG results with those of
already published works using atomistic MD). Using the previous
suggestions, my new pull code is the following:
By "pull apart," do you mean to unwind the secondary structure of the prote
Hi again,
I am trying to pull apart a CG protein (to verify CG results with those of
already published works using atomistic MD). Using the previous
suggestions, my new pull code is the following:
title= Martini
cpp = /usr/bin/cpp
integrator
With distance you could be unlucky that it takes the distance
in the opposite direction.
Berk
> Date: Fri, 31 Jul 2009 12:32:13 +0200
> From: alexander.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] pulling
>
> Thx for the quick reply!
>
> I use
same answers if you do not have pbc issues.
>
> Berk
>
> > Date: Fri, 31 Jul 2009 12:13:07 +0200
> > From: alexander.h...@mytum.de
> > To: gmx-users@gromacs.org
> > Subject: [gmx-users] pulling
> >
> > Hey,
> >
> > I appear to have serious trouble
answers if you do not have pbc issues.
Berk
> Date: Fri, 31 Jul 2009 12:13:07 +0200
> From: alexander.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pulling
>
> Hey,
>
> I appear to have serious trouble understanding how to set up the pulling
>
Hey,
I appear to have serious trouble understanding how to set up the pulling
properly.
I have many configurations of a protein partially adsorbed to a froozen
surface (the configs differ
in the amount of the protein that has been desorbed).
Now I want the pulling to keep the distance of the deso
Hi XAvier, Marc, and David,
Thank you so much for the reply and encouragement ;-). Please forgive me
as I am trying to learn how to reply to the thread that I started. With
regards to the fun discussion, it was my original intent to compare the
results of pulling with the MARTINI forcefield (if th
Hi,
Just picking up the following bits of the conversation:
David van der Spoel wrote:
>> What does this boil down to? If you want to apply MD tools to get
>> an accurate force curve *now*, use all atom models. [..]
x.peri...@rug.nl said:
>> This is of course the idea, but then comes the probl
On Jul 30, 2009, at 12:10 PM, David van der Spoel wrote:
XAvier Periole wrote:
On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote:
Marc Baaden wrote:
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point
out
that we have used CG models to pull on the
XAvier Periole wrote:
On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote:
Marc Baaden wrote:
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point out
that we have used CG models to pull on them and at least qualitatively
they behave quite reasonably, a
On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote:
Marc Baaden wrote:
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point out
that we have used CG models to pull on them and at least
qualitatively
they behave quite reasonably, although these models
Marc Baaden wrote:
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point out
that we have used CG models to pull on them and at least qualitatively
they behave quite reasonably, although these models have never been
parameterized or systematically tested with t
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point out
that we have used CG models to pull on them and at least qualitatively
they behave quite reasonably, although these models have never been
parameterized or systematically tested with this kind of applicat
Hi Johnny,
I am not familiar with pulling and even less with gromacs but I would be
very cautious in using the MARTINI force field for the kind of
simulation
you are doing.
This CG model has not been tested at all for this and it might not be
very good at it! But I would be very interested in
Dear gromacs users,
Hi, I am trying to pull apart a relatively large protein (CG using the
martini force field) by pulling on two groups in opposite directions. To
do this, I will be using the following .mdp file. However, I am almost
certain that it contains errors:
title= Ma
wara boon wrote:
Dear, gmx-users
I can't pull molecule into DPPC lipid bilayer. I want file.mdp
to use MD simulations.
Please.
That won't fix your problems. If you need to learn, do some tutorials
and read some documentation and try things out.
Mark
__
Dear, gmx-users
I can't pull molecule into DPPC lipid bilayer. I want file.mdp to use
MD simulations.
Please.
From
Wara
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Plea
Dear Sir,
I want to pull a molecule called PRO from the lipid membrane
DPP. To do this I have written the .mdp file as following from the help of
gromacs mannual 4.0 . But when I try to make .tpr file from the .gro file,
it says that "segmentation fault".
Can you please wr
OMACS users
Sent: Wednesday, November 19, 2008 1:57:19 PM
Subject: Re: [gmx-users] Pulling in 4.0 - Any documentation?
Semen Esilevsky wrote:
> Dear All,
> Where can I find documentation about the pull code in Gromacs 4.0? As far as
> I understand old style of setting up pulling simulati
Semen Esilevsky wrote:
Dear All,
Where can I find documentation about the pull code in Gromacs 4.0? As far as I understand old style of setting up pulling simulations in separate file does not work any more, but I can't figure out how to transfer pulling params correctly to mdp file.
Any help is
Hi,
Currently there is a beta 4.0 manual on ftp.gromacs.org.
The mdp options can also be found in:
share/html/online/mdp_opt.html
Berk
> Date: Wed, 19 Nov 2008 03:33:47 -0800
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Pulling in 4.0 - Any d
Dear All,
Where can I find documentation about the pull code in Gromacs 4.0? As far as I
understand old style of setting up pulling simulations in separate file does
not work any more, but I can't figure out how to transfer pulling params
correctly to mdp file.
Any help is appreciated!
P.S. Pr
Hi Mareike,
Probably your simulation starts off with remapping your pull-atom over
the periodic boundaries. Make sure that the atom and the protein are
properly placed inside the rhombic dodecahedron (actually the brick
representation of it) before the simulation. Note that Gromacs
performs mappi
Hallo!
I have got a question on the afm pulling option. I am trying to pull a single
atom into the direction of the center of mass of a protein in my simulation
cell. Everything works fine with a cubic box. When I use a truncated
dodecahedral box, at time step 1 the atom is suddenly located at
Giacomo Bastianelli wrote:
Dear Users,
I would like to use a force that during the dynamics
will bring closer my two molecules.
Is there any way to implement this function?
Section 6.2 of the manual.
Mark
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Dear Users,
I would like to use a force that during the dynamics
will bring closer my two molecules.
Is there any way to implement this function?
Thanks in advance,
Giacomo Bastianelli
___
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http://www.gro
Hi, I would like to measure a force-strain behaviour for a molecule along a certain axis. I fixed one end of the molecule. I am pulling the other end using a pull group containing C-alphas. My problem is that different parts of the molecule do not have the same flexibility - in particular, one
My pull.ppa file is as follows.
verbose = noruntype = afmgroup_1 = Fe group_2 = His93reference_group = 4Nweights_1 = 55.847 reference_weights = 14.0067 14.0067 14.0067 14.0067weights_2 = 14.0067 1.008 12.011 12.011 12.011 14.0067 1.008 12.011 12.011 14.0067 12.011 15.9994reftype = comreflag = 1pull
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