Hi,
I believe there is no force output for constraint pulling. Try umbrella.
Erik
On Mar 18, 2013, at 3:28 PM, raghav singh wrote:
Hello Fellow Users,
I am trying to pull a DNA molecule. I have fixed one end and trying
to pull
the other one using this .mdp file.. force output is all zeros
[gmx-users-boun...@gromacs.org] on behalf
of Justin Lemkul [jalem...@vt.edu]
Sent: Friday, November 02, 2012 5:04 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Pull code, Velocity distribution
On 11/2/12 10:52 AM, Samadashvili Nino wrote:
> Hello,
>
> I have
[jalem...@vt.edu]
Sent: Friday, November 02, 2012 5:04 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Pull code, Velocity distribution
On 11/2/12 10:52 AM, Samadashvili Nino wrote:
> Hello,
>
> I have been using the pull code for friction calculations. I am not
On 11/2/12 10:52 AM, Samadashvili Nino wrote:
Hello,
I have been using the pull code for friction calculations. I am not
doing umbrella sampling but just pulling one slab of crystal on top of another
with the constant velocity. I would like to know how Gromacs is calculating
the pu
On 2012-10-04 11:50, Emma Eriksson wrote:
Dear all,
I am using the pull code in Gromacs 4.5.5 to constrain the distance in one
direction (z) between a small molecule and a lipid bilayer. I run separate
simulations with distances 0-4 nm constrained. I use pull_geometry = cylinder.
The pull par
Hello,
I was following your argument but then doesnt pull_dim=Y Y Y mean it pulls in
all directions at once? I use pull_dim=N N Y , or just 1 pull direction and it
works. I might be wrong, but would be interesting if you got it to work like
that for a small molecule.
Stephan Watkins
---
--- Begin Message ---
Hi Thomas
I am sorry to bother you but if you could answer a few questions I have
about how the pull-code works with respect to my system I would really
appreciate it.
My system is a liquid and I am trying to pull one substituent of one
liquid molecule in a certain region of
Hi Thomas
A few points below under your points
Thomas Schlesier wrote:
> Yes you are right, should be between 0 and >0.
>
> Do you have a window for a distance equal 0?
Yes
>
>
> This window should behave similar to the RDF-analysis. Because there
> are "no directions".
It doesn't. By this I mea
Hi Thomas
I am sorry to bother you but if you could answer a few questions I have
about how the pull-code works with respect to my system I would really
appreciate it.
My system is a liquid and I am trying to pull one substituent of one
liquid molecule in a certain region of another liquid molecul
Hi Thomas
Many thanks for the reply again. At larger distances the two curves
match up quite well. The curve from the reversible work theorem is
better behaved and smoother but this could be solely due to statistics.
I am slightly confused about your statement
"If the small circle moves between 0
Dear Chris,
Thank a lot for your reply. I am trying the pull code that you have suggested.
And I would be more specific about the problem and code in my future mails.
regards,
Shilpi
On 02/10/11, chris.ne...@utoronto.ca wrote:
> Dear Shilpi:
>
> Can you use something like this?
>
> pull
Shilpi Chaurasia wrote:
Dear Justin,
Thanks a lot for your reply.
Here I am providing the data and explaining the problem in detail:
I hope that it will help you in understanding in a better way.
Considering the tetramer as 'abcd'. 'ab' as one dimer and 'cd' as
another, I want to separate
Dear Justin,
Thanks a lot for your reply.
Here I am providing the data and explaining the problem in detail:
I hope that it will help you in understanding in a better way.
Considering the tetramer as 'abcd'. 'ab' as one dimer and 'cd' as
another, I want to separate 'ab' and 'cd'. Length o
Shilpi Chaurasia wrote:
I am trying to pull apart two dimers of tubulin protein joined
together, to form two separate dimers by steered molecular dynamics
using Pull code. The objective is to separate the dimers by pulling
along one axis only (Y axis). I ran the simulation for 25 ps and it
Sent: 10 February 2011 12:33
To: Gromacs Users' List
Subject: Re: [gmx-users] pull code
Poojari, Chetan wrote:
Hi Justin,
Thank you very much for your suggestions. I will use constraint force to
force a peptide into a membrane with pulling for longer time.
yes with "POSRES_LIPID&
mkul [jalem...@vt.edu]
Sent: 10 February 2011 12:33
To: Gromacs Users' List
Subject: Re: [gmx-users] pull code
Poojari, Chetan wrote:
> Hi Justin,
>
> Thank you very much for your suggestions. I will use constraint force to
> force a peptide into a membrane with pulling for longer
st for
GROMACS users Subject: Re: [gmx-users] pull code
Poojari, Chetan wrote:
Hi,
I am using umbrella sampling to pull my peptide (peptide starting from
above the lipid bilayer) into the hydrophobic core of the lipid bilayer.
Following are my inputs i have used:
title = Umbrella pulli
ubject: Re: [gmx-users] pull code
Poojari, Chetan wrote:
> Hi,
>
> I am using umbrella sampling to pull my peptide (peptide starting from above
> the lipid bilayer) into the hydrophobic core of the lipid bilayer.
>
> Following are my inputs i have used:
>
> title
Poojari, Chetan wrote:
Hi,
I am using umbrella sampling to pull my peptide (peptide starting from above
the lipid bilayer) into the hydrophobic core of the lipid bilayer.
Following are my inputs i have used:
title = Umbrella pulling simulation
define = -DPOSRES_LIPID
; Ru
bv07ay wrote:
Hello,
i am having trouble using the pull options in gromacs 4.0.4. i am
simply trying to move a protein from the top of the box to a certain
point in the center. i have had no luck using a constant pulling or
umbrella pulling the error i receive is:
"You are using an absol
Hi Justin
Thanks for your help. The two molecules are now moving together. I am
however slightly confused about the parameters pull_rate1 and pull_k1. I
want the molecules to come together very slowly therefore
I would set the rate to be a very small value. How the does the force
come into play an
Gavin Melaugh wrote:
Hi Justin
Thanks. If I use the pull_geometry = direction I would go for the
following jus t to pull the molecules together in the z direction.
pull= umbrella
pull_geometry = direction
pull_start = yes
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull
Hi Justin
Thanks. If I use the pull_geometry = direction I would go for the
following jus t to pull the molecules together in the z direction.
pull= umbrella
pull_geometry = direction
pull_start = yes
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_vec1 = 0.0 0.0 -1.0
pull
Gavin Melaugh wrote:
Hi all
I am commencing the initial stages for he calculation of potential of
mean force of bringing together two cage molecules. I am following the
tutorial in such an exercise at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
Hi,
With only 1 pull dimension active (through pull_dims) all three geometries are
equivalent.
In 2 or 3D there are all different.
With pull_geometry=direction the pull force is the force working along the
direction vector.
So in general you can't incorporate the direction (only sign in your c
Hi,
I would still say pull_geometry=direction would be the easiest solution for
this case,
but pull_geometry=position will probably do the same thing.
Berk
> Date: Sun, 15 Nov 2009 17:11:43 -0500
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull code with
Hi,
Sorry, but I have no clue what you mean with sampling >0
and how you would end up with a bimodal distribution.
You don't mean the box 0, do you?
That is irrelevant.
What can be a problem is that you pull distance should not be more than half
the box length.
Berk
> Date: Sun, 15 Nov 2009 1
Hi,
I only now noticed Justin mail on g_wham.
You can probably also use pull_geometry=distance and pull_init=1,
if you starting structure has group1 close to 1 nm below group 0.
Berk
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] pull code with defined negative
Hi,
pull_init should be 1, not 4.75, if you want group1 to be 1 nm below group0.
Alternatively you can have vec = 0 0 1 and pull_init = -1.
Berk
> Date: Sat, 14 Nov 2009 14:54:54 -0500
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull code with defined nega
Berk Hess wrote:
Hi,
You should use pull_geometry=direction.
distances don't get negative.
I think this presents a problem if one is intending to use g_wham to calculate
PMF from the umbrella sampling protocol. When using direction for
pull_geometry, g_wham fails with a fatal error:
---
Hi,
You should use pull_geometry=direction.
distances don't get negative.
Berk
> Date: Sat, 14 Nov 2009 09:21:39 -0500
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull code with defined negative relative displacements
>
> Hello, I am re-running some of ou
: Re : [gmx-users] PULL CODE AND NpT ensemble
Date: Thu, 27 Aug 2009 08:03:56 -0400
From: gigita...@aol.fr
Hi Berk,
Thanks for your answer. I just want to be sure that the procedure is correct.
No I do not look at the pressure/volume fluctutation. But I do want to make a
clever choice of the
Berk Hess
A : Discussion list for GROMACS users
Envoyé le : Jeudi, 27 Août 2009 13:45
Sujet : RE: [gmx-users] PULL CODE AND NpT ensemble
Hi,
I would use v-rescale and Berendsen pressure coupling.
Although Berendsen pressure coupling, strictly speaking, does not give the
correct ensembl
Hi,
I would use v-rescale and Berendsen pressure coupling.
Although Berendsen pressure coupling, strictly speaking, does not give the
correct ensemble,
in practice it produces negligible artifacts, unless you are looking at
pressure/volume fluctuations.
Berk
To: gmx-users@gromacs.org
Date: Th
Hi,
First, please switch to 4.0.5, I have put several fixes in the pull code
in the 4.0 minor releases.
You did not specify pull_init1, nor pull_start, this means you start pulling
at a distance of 0, which means the center of the bilayer.
Setting
pull_start = yes
should fix your problem.
Berk
Hi,
Maybe there is an older grompp in your path.
Type grompp -h to see which version you are using.
And:
which grompp
to see where it comes from.
Berk
> Date: Mon, 11 May 2009 13:03:07 +0300
> From: neamtuand...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pull code problem
>
>
Hi,
Do you have another line with "pull =" somewhere in your mdp file?
PS You should switch to Gromacs 4.0.4, since it contains several small
bug fixes for the pull code.
Berk
> Date: Mon, 11 May 2009 12:38:35 +0300
> From: neamtuand...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-use
Hi,
I have no clue why you would want to fix the peptide in the middle of the box.
But what you want seems to be more like com removal for the peptide only
with the comm options.
The pull code will do approximately what you want, but with pressure coupling
there is the problem that your peptide w
Hi Justin:
1) EXTREMELY IMPORTANT: I already know of 1 person, but is anyone alergic to
either Iodine or Chlorine?
No, I am not alergic to those compounds. The only thing that I am alergic is
Penicillin and Ampicilin.
2) Any other medical problems?
No
3) An Emergency contact person.
Fernand
Hi Rodney,
the other alternative is to define the springs in your topology file.
You first need to merge
your groups (is part of different molecules) and run the different
combination you need by
defining them by hand; you can easily write a awk script to generate
the different topologies
This seems to be a good reference for soft-core interactions.
BEUTLER et al. AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN
FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS. Chem Phys
Lett (1994) vol. 222 pp. 529-539
On Thu, Feb 12, 2009 at 1:33 PM, wrote:
Does anybody know of a
avinash kumar wrote:
Hello all,
does anybody possess a sample of "pull.pdo" data file for pull codes.
The pull.pdo file is output, are you sure that's what you want, or do you want a
pull.ppa input file? Either way, enter "pull.pdo" or "pull.ppa" into the Search
page for the archive and
Hi,
If you pull without a reference, you will be doing nothing in the limit
of slow pulling. For fast pulling you will be doing something.
pull_start=yes
pull_init1=0
will initialize set pull_init to the initial distance.
Berk
> Subject: RE: [gmx-users] Pull Code problems
> From
orce on the COM of the whole system.
>
> The AFM option is no longer there.
> I never understood what the difference between Umbrella and AFM was.
> But Umbrella (as well as constraint) should be able to do all things
> that were possible before (and more).
>
> Berk
>
&
to do all things
that were possible before (and more).
Berk
> Subject: Re: [gmx-users] Pull Code problems
> From: gene...@gmail.com
> To: gmx-users@gromacs.org
> Date: Tue, 13 Jan 2009 18:44:36 +0300
>
> OK,
> I have a new problem.
> I`ve started the simulation
OK,
I have a new problem.
I`ve started the simulation with the following pull parameters
;---PULL CODE -
pull<-->=<-> umbrella
pull_geometry<->= direction
pull_group0<-->= r_500
pull_group1<--->= r_535
pull_vec1<->= -1.306 1.355 -0.319
pull_k1><-->= 1000
Hi,
pullx.xvg has the coordinates of group 0 and the distances
of the other groups to group 0.
pullf.xvg has the force of the umbrella potential
which works along the direction vector you gave,
this can be positive or negative depending on the direction.
Berk
> Subject: RE: [gmx-users] P
OK,
I did some homework and now I`m up to this:
;---PULL CODE -
pull= umbrella
pull_geometry = direction
pull_group0 = r_500
pull_group1 = r_535
pull_vec1 = -1.306 1.355 -0.319
pull_k1 = 1000
pull_rate1 = 0.5 ; nm/ps Extreme para
Hi,
You don't indicate which xvg file was 0, I guess pullf.xvg.
Could it be that you did not specify a force constant, meaning fc=0?
Berk
> From: gene...@gmail.com
> To: gmx-users@gromacs.org
> Date: Tue, 13 Jan 2009 14:26:47 +0300
> Subject: [gmx-users] Pull Code problems
>
> Hello,
>
> I am
Mark,
I just checked and it seems I was consulting a manual for an older version
than 3.3.1! I guess it was taken out in 3.3.1
Sorry for not being more careful.
Thank you.
-Dina
On 10/20/07 4:16 PM, "Mark Abraham" <[EMAIL PROTECTED]> wrote:
> dtmirij wrote:
>> I searched the on line document for
dtmirij wrote:
I searched the on line document for runtype and got nothing. But in the
Manual in chapter 6 there is an overveiw of the pull code options and one of
the options listed is the "starting structures" and it says the keyword for
runtype to use for this is "start".
http://www.gromac
I searched the on line document for runtype and got nothing. But in the
Manual in chapter 6 there is an overveiw of the pull code options and one of
the options listed is the "starting structures" and it says the keyword for
runtype to use for this is "start".
On 10/19/07 6:55 PM, "Mark Abraham
dtmirij wrote:
Hello everyone,
I just want to clarify if the runtype "start" option works in gromacs-3.3.1.
I didn't see anything in the mailings list suggesting that it doesn't.
Did you try searching the manual for "runtype"?
Mark
___
gmx-users mai
I'm no umbrella user, but as far as I know, you have to set different
parameters, according to the manual. These may be similar to the AFM
parameters, but still, in the config file, they are separated.
Sure, you don't define a pull rate for Umbrella, because you build, as
you said, discrete syst
Hi Maik,
Thank you for the answer. I still have some questions.
I still didn't get the umberalla sampling method. It seems to me AFM and
umberalla are the same except that in umberalla we dont define a Pull
rate. Looking at the literature, people have been using umberalla method
with discrete sim
Hi
You have to tell GROMACS in the parameters-file (.ppa) which kind of PMF
you want to calculate (runtype=afm,umbrella). Depending on this choice
it's very likely that the afm_rate is simply ignored for umbrella, no?
The force constant is mimicking the stiffness of the spring. You want to
o
Thank you Chris for providing recognition of this issue.
-Steve
Chris Neale wrote:
I have encountered noticeable differences while using the pull code
with the -shuffle -sort options in parallel, as opposed to running in
serial or in parallel without the options. Using -shuffle -sort, the
dy
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