Commenting out the gmx_fatal() call in src/mdlib/pull.c, line: 331 and
recompiling grompp and mdrun
allows the run to proceed. Everything is stable for 250 ps. I will report if it
fails.
I have posted a redmine at: http://redmine.gromacs.org/issues/1352
Thank you,
Chris.
-- original message
Dear Users:
I am trying to use the pull code to add a constant force in a particular
direction.
I am getting an error that the initial distance is greater than 1/2 the box
size.
(error in 4.5.5, 4.6.1, 4.6.3)
I must not understand how to use this. I checked the online .mdp options:
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.
I have tried going through the user-list but have not found any solution
yet. I am using gmx-version 4.5.5.
Any idea why is it
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
-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 been using the pull code
[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
doing umbrella
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 pulling force (pullf.xvg) during sliding. Is the
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
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
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 parameters are the following:
pull
Hi,
I try to pull the small molecule from the bulk solution to the surface by the
Constraint function.
However, it seems that it does not work well.
Here my part of run parameters about the Constraint in my mdp file
##
constraints = all-bonds; hbonds; all-bonds
Hello everybody, I have used pull code to separate two molecules in water.
The idea is to generate initial configurations for umbrella sampling.
Initially I tried to use pull_geometry=distance. I noticed that the vector
connecting
the two molecules are not remained on the main axis of the box (z).
Hello All,
I am trying to apply pull code on DNA I-motif structure which is 4 stranded
DNA with the pair of 2 parallel duplexes arranged in anti-parallel manner. I
have followed the tutorial by Justin Lemkul it works well but I have to
select the fixed and pull group on different chains
Hi all
I am returning to a query I had a few weeks ago regarding a discrepancy
between two free energy curves. One calculated using umbrella sampling,
the other calculated via the reversible work theorem from the RDF. There
is sufficient sampling of the dynamics in the RDF so this method is
Hi Gavin,
if i remember correctly it was a system about pulling a ligand from a
binding pocket?
To make the system simpler we have a big circle and in the middle a
small circle. And we assume that the potential minimum for the
interaction between both circles is when the small cirlce is in the
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
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
Yes you are right, should be between 0 and 0.
Do you have a window for a distance equal 0?
This window should behave similar to the RDF-analysis. Because there are
no directions.
Or to reformulate the problem.
We make an umbrella window for a distance of 1. If particle stays there
everything
Original-Nachricht
Datum: Fri, 17 Feb 2012 16:34:22 +0100
Von: Thomas Schlesier schl...@uni-mainz.de
An: gmx-users@gromacs.org
Betreff: [gmx-users] pull-code
Hi Gavin,
if i remember correctly it was a system about pulling a ligand from a
binding pocket?
To make the system
be wrong, but would be interesting if
you got it to work like that for a small molecule.
Stephan Watkins
Original-Nachricht
Datum: Fri, 17 Feb 2012 16:34:22 +0100
Von: Thomas Schlesier schlesi at uni-mainz.de
An: gmx-users at gromacs.org
Betreff: [gmx-users] pull-code
Hi
Dear all,
I have a problem using the pull code in Gromacs 4.5.1. I am running simulations
with a small molecule at constrained distances from the bilayer center in a
membrane (z-direction) in order to calculate permeability data. I use the force
acting on the molecule (pullf.xvg) at different
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
Dear Shilpi:
Can you use something like this?
pull = umbrella
pull_geometry= position
pull_dim = N N Y
pull_vec1= 0 0 0
pull_start = no
pull_ngroups = 1
pull_group0 = PRO-1
pull_pbcatom0
Dear Gmx users,
I am
studying the interaction between the tubulin protofilaments arranged
in parallel. For this operation, I have considered a tetramer and a dimer from
two protofilaments
respectively (say PRO-1 and PRO-2), tetramer in PRO-1 and a dimer in
PRO-2. I want to
move the dimer of
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
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
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 accomplished well but while
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
: 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 i am keeping
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 i am keeping the lipids rigid while pulling
: [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 pulling simulation
define
: 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 pulling simulation define
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
; Run parameters
integrator
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
;
Dear All
Sorry wrong subject title in previous post. Can someone please tell me how to
generated the plot of mean force
having ran the pull code at several distances using constraints?
Gavin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Does anyone know if the pull code can be used to determine structure stability?
If I wanted to generate a stress-strain plot of an alpha-helix, would the pull
simulation give me the data such as the force vs displacement?
Thanks
--
gmx-users mailing
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 absolute reference
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
Hi all,
Could anybody please share some working system to look at the pull
code in gromacs? I did not find any examples in the WWW,
unfortunately.
Vitaly
--
Dr. Vitaly Chaban
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search
I'd send a list of links except that the other end of a google search for
gromacs pull code example
has all of what you will need to broaden your general pull code
understanding. The mailing list has an absolutely massive number of
posts on this too.
Chris.
Hi all,
Could anybody please
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
Hi all
I am using the pull-code to pull two molecules are together which is working. 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
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
In contrast to the
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 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
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
and other parameters set appropriately.
Chris.
-- original message --
Gavin Melaugh gmelaugh01 at qub.ac.uk
Wed Jun 30 18:27:47 CEST 2010
* Previous message: [gmx-users] the job is not being distributed
* Next message: [gmx-users] Pull code
* Messages sorted by: [ date ] [ thread
Hi Berk,
I have done the tests and you are entirely correct. I have one further
question: If I simply want to pull to a relative displacement of -1.0
nm, is there any reason to prefer one of these methods, or are they
just overlapping implementations of different methods that also have
case) into
the force,
unless you would print the whole vector.
Berk
Date: Wed, 18 Nov 2009 12:12:49 -0500
From: chris.ne...@utoronto.ca
To: gmx-users@gromacs.org
Subject: [gmx-users] pull code with defined negative relative displacements
Hi Berk,
I have done the tests and you
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
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
, 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 negative relative displacements
Hi Justin
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.
Agreed, although this will not work when the force constant is not
strong enough to inhibit any sampling 0 -- wherein
:33:30 -0500
From: chris.ne...@utoronto.ca
To: gmx-users@gromacs.org
Subject: [gmx-users] pull code with defined negative relative displacements
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
?
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 12:33:30 -0500
From: chris.neale at utoronto.ca
To: gmx-users at gromacs.org
Subject: [gmx-users] pull code with defined negative relative
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
Hello, I am re-running some of our gromacs 3 simulations using gromacs
4, and as far as I can tell the gromacs 4 pull code, while very nicely
enhanced from gromacs 3, has also lost some functionality.
I am calculating the PMF of a peptide across a bilayer and, to
simplify the issue, what I
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 our
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:
-users] pull code with defined negative relative displacements
Hello, I am re-running some of our gromacs 3 simulations using gromacs
4, and as far as I can tell the gromacs 4 pull code, while very nicely
enhanced from gromacs 3, has also lost some functionality.
I am calculating the PMF of a peptide
Hi all,
I would like to use pull code to evaluate the free energy of pulling system1
from system2. Free energy calculation should be done for NpT ensemble. All
tutorials found for calculating free energy used
1) berensen for T and P coupling or
2) berensen for T coupling AND Parrinelo for P
: Thu, 27 Aug 2009 07:20:00 -0400
From: gigita...@aol.fr
Subject: [gmx-users] PULL CODE AND NpT ensemble
Hi all,
I would like to use pull code to evaluate the free energy of pulling system1
from system2. Free energy calculation should be done for NpT ensemble. All
tutorials found for calculating
Hess g...@hotmail.com
A : Discussion list for GROMACS users gmx-users@gromacs.org
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
: 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
.
Berk
Date: Thu, 6 Aug 2009 10:49:26 +0800
From: djpit...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] pull code problem
Hi, all:
I tried to pull a specific DPPC, say, r3, out of a pre-equilibrated bilayer
into the water along the positive z axis. For the pull code parameters, I used
Hi, all:
I tried to pull a specific DPPC, say, r3, out of a pre-equilibrated bilayer
into the water along the positive z axis. For the pull code parameters, I
used:
pull = umbrella
pull_geometry= distance
pull_vec1 = 0. 0. 1.
pull_dim= N
hello,
I am trying to do a pulling simulation with gromacs 4.0.2
I added the following lines to the .mdp input file for grompp:
...
pull = constraint
pull_geometry = distance
pull_dim = Y Y Y
pull_nstxout = 10
pull_nstfout = 10
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-users
Hi Berk,
thank you for the reply
here is my mdp file:
;
; User aneamtu
; Joi, 7 mai - 2009
; Input file
;
title = Production_runs
;define = -DPOSRES -DPOSRES_CA2+_IONS
;constraints = all-bonds
integrator
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
Sorry it appears that something was wrong with my .mdp file .. Idon't
know what ...but I wrote again the pull code lines and the warnings
dissapeared.
Thank you again,
Andrei
___
gmx-users mailing listgmx-users@gromacs.org
artifacts when you change
the pull position too fast.
Berk
Date: Thu, 16 Apr 2009 10:27:04 -0400
From: chris.ne...@utoronto.ca
To: gmx-users@gromacs.org
Subject: [gmx-users] pull code absolute reference artifacts
Hello,
I have a question about the following grompp 4.0.4 warning:
You
freely move,
thus the net effect is zero, except for lots of nasty artifacts when
you change
the pull position too fast.
Berk
Date: Thu, 16 Apr 2009 10:27:04 -0400
From: chris.neale at utoronto.ca
To: gmx-users at gromacs.org
Subject: [gmx-users] pull code absolute reference artifacts
Hello,
I
Hello,
I have a question about the following grompp 4.0.4 warning:
You are using an absolute reference for pulling, but the rest of the
system does not have an absolute reference. This will lead to
artifacts.
While I do realize that this is an excellent error message containing
lots of
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.
Hello everybody:
I am trying to perform some PMF calculations using the pull code with a spring
(umbrella sampling) but using two reaction coordinates (E1 and E2) between four
different groups (r1,r2,r3 and r4).
All the examples and tutorials that I found so far on the web, only mention PMF
Hi Rodney,
This may be possible if your reference is absolute coordinates. In this case, just use pull group 1 and 2, with the
reference group undefined. For more nuanced usage, the problem is that you are only allowed one
reference group (and one type of pull code usage) in a given run.
I
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
Hello,
I see from looking at the source code that the free-energy lambda
dependence is now available to the pull code based on pull_kB1.
However, this leads to serious problems converging near lambda=1 when
pull_k1=large and pull_kB1=0 and in the absence of a restraint (with
k=0) the
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, chris.ne...@utoronto.ca wrote:
Thank you Matt, that is indeed the perfect paper. I'll post back here
once I figure out exactly where the (1-lambda)^2 term would fit into
the pull code US equation.
Chris.
This seems to be a good reference for soft-core interactions.
BEUTLER et al. AVOIDING SINGULARITIES AND NUMERICAL
Hello all,
does anybody possess a sample of pull.pdo data file for pull codes.
--
Avinash Kumar.
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
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 you
Hello,
I was running different simulations with the following pull code
1/
;---PULL CODE -
pull= umbrella
pull_geometry = direction
pull_group1 = r_535
pull_vec1 = 0.51 0.026 0.273
pull_k1 = 110
pull_rate1 = 0.002 ; nm/ps = 20 A/ns
Hello,
I am trying to run a pulling simulation with gromacs 4.0.2.
I have appended the following pull code to the mdp file:
;---PULL CODE -
pull= umbrella
pull_geometry = direction
pull_group0 = r_500
pull_group1 = r_535
pull_vec1 = -1.306
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 trying
2009 14:26:47 +0300
Subject: [gmx-users] Pull Code problems
Hello,
I am trying to run a pulling simulation with gromacs 4.0.2.
I have appended the following pull code to the mdp file:
;---PULL CODE -
pull = umbrella
pull_geometry = direction
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 trying
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
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 with the following pull parameters
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
Subject: Re: [gmx-users] Pull Code problems
From: gene
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: gene
Using gromacs 3.3.1: I am currently trying to using the pull code to do
non-equilibrium simulations that will remove a ligand from a binding pocket in
a directionally unbiased manner. As far as I can tell, some type of harmonic
distance restraint is not possible using center of mass that has a
My appologies, I wasn't doing mass weighting to determine the initial offset.
It works perfectly with a loop like this in g_com.c:
clear_rvec(coms);
coms_count=0.0;
for(i=0; inidx; i++){
coms[XX]+=fr.x[index[i]][XX]*top.atoms.atom[index[i]].m;
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:
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.
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
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.
If I have
runtype = start
in my pull.ppa file then gromacs gives me an error:
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
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
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