I think you should add -tau 0 when using flooding as harmonic restraint
(since you do not want the flooding potential to change).
Okay, adding -tau 0 does turn it properly into a harmonic potential,
according to edsam.xvg. However, the average position of the resulting
(gaussian) is near but not
Why not do two umbrella sampling simulations: one with initial conformations
from your faster pulling and one with initial conformations from your slower
pulling. Then you can run them both as regular US simulations until (a) neither
US PMF is drifting systematically with increasing simulation t
Think your .mdp-file looks reasonable.
If you are totaly unsure you could determine the PMF of two water
molecules. As a reference one can use the radial distribution function
g(r) and calculate the PMF as
V_pmf(r) = -kT LN(g(r))
One side note:
Since the force constant you are using is relativ
Friday, July 12, 2013 9:04 PM
Subject: [gmx-users] Re: Umbrella Sampling settings
In GROMACS groups are called via the *.ndx file (default: index.ndx)
Be aware that 'pull_dim' determines in which diretions (x,y,z) the
umbrella potential acts. So use N N Y , if you want that the ion can
s" (Y).
So what should I do?!
Sincerely,
Shima
- Original Message -
From: Thomas Schlesier
To: gmx-users@gromacs.org
Cc:
Sent: Friday, July 12, 2013 9:04 PM
Subject: [gmx-users] Re: Umbrella Sampling settings
In GROMACS groups are called via the *.ndx file (default: inde
In GROMACS groups are called via the *.ndx file (default: index.ndx)
Be aware that 'pull_dim' determines in which diretions (x,y,z) the
umbrella potential acts. So use N N Y , if you want that the ion can
move freely (onsidering the pull) in the xy-plane and Y Y Y if you want
to also restrit th
But you need each of these lines for both cases (SMD and US). Probably
one could skip two lines and use the default values, but it's better to
set them manually. See below for comments (comments are under the
related entry):
Thanks for your reply. But when I don't understand why these extra
Generally:
Using a higher force constant and / or pulling velocity drives the
system faster out of equilibrium, which results in higher rupture forces.
Varying the force constant has two effects. The softer the potential is,
the larger are the fluctuations in the coordinates but the lower are th
Sorry, my writing was not really excat.
If you use a reference group, the force / potential acting on the pulled
group is always relative to the reference group.
If you use 'pull_geometry = distance' the origin potential is always in
the distance 'pull_init1' along the vector from the reference
Dear Thomas,
>> In AMBER I remember I did once methane-methane interaction, just
distance based umbrella sampling. But there I did not
>> provide any direction. So should it not be N N N in Gromacs if I want
to allow them freely move in xyz.
Sorry am wrong that should be Y Y Y in Gromcacs! for su
Dear Thomas,
Thanks a lot again for great reply. Please clarify this also,
>> If one uses only 'Y N N' B would only move along the x-axis due to the
pull, but could move freely in the yz-plane
>>You never want to use the pull-code and 'pull_dim = N N N'
>>This would mean that there is no force ac
For comments to your questions see below.
More general: (somewhat longer than i wanted. Hope you find some answers
here)
Imagine two interacting particles A and B which are alinged to the
x-axis. We take A as the reference group, B as pulled group and put the
origin of the umbrella potential
Dear Thomas,
Thanks a lot for your time and nice explanation. I was not able to get
specially the pull_start flag but now its quite clear.
I feel sorry, that should be pull_dim = N N N in my case. Also I will be
much thankful if you please can help me to make understand following:
1)
>> If you d
Look also into the manual. But the tutorial is a nice place to start.
For further comments see below:
Dear Lloyd,
I have read that but my system is different
regards,
On Thu, May 30, 2013 at 8:28 PM, lloyd riggs wrote:
>Dear Jiom,
>
>Look at justines tutorial, there's example pull .mdp.
>
Hi,
it seems that you've only coupled your protein to the thermostat, but
not the solvent, hence the error message.
Generally one would couple both domains of the protein to one thermostat
and the solvent (inluding ions) to another thermostat.
Side note: If you want to use the WHAM method for
>--
>
>Message: 1
>Date: Wed, 20 Mar 2013 12:55:45 +0100
>From: Thomas Schlesier
>Subject: [gmx-users] Umbrella sampling with large pulling distance
>(larger than half of the box size)
>To:
>Message-ID: <5149a3c1.2000...@
Restating of my question about ussage of essential eigenvectors as the
pulling coordinates I'd like to introduce some example.
The case study is the open to close transition in some protein. For
instance by means of essential dynamics sampling technique (in
targeted-contraction mode) I've simulated
Thanks Erik!
/PK
2012/11/16 Erik Marklund
> Hi,
>
> Blindly defining the center of mass for a group of atoms is not possible
> in a periodic system such as a typical simulation box. You need some clue
> as to which periodic copy of every atom that is to be chosen. By providing
> pull_pbcatom0 y
Hi,
Blindly defining the center of mass for a group of atoms is not possible in a
periodic system such as a typical simulation box. You need some clue as to
which periodic copy of every atom that is to be chosen. By providing
pull_pbcatom0 you tell gromacs to, for every atom in grp0, use the pe
Hi Chris
Seems my confusion was that I assumed that the distances in the
profile.xvg-file should correspond to something I could measure with
g_dist. Turns out it does not.
Thank you for helping me sorting out this, I got it now :-)
About pull_pbcatom0 though. My box is >> 2*1.08 nm in all direct
Hi Erik,
Thank you for your answer.
I see your point now. Went and had a look in gmx_wham.c to see how things
are calculated, and that makes sense.
I was looking for an easy way of relating different parts of the resulting
PMF to my original starting frames, as a means to understand exactly what
Hi,
See below.
14 nov 2012 kl. 15.06 skrev Gmx QA:
> Hi Chris,
>
> and thank you for your reply. I should have included my g_dist command in
> my first mail. Here goes:
>
> I first run trjconv to extract the individual frames from my pulling
> trajectory
> $ trjconv -f pull.xtc -s pull.tpr -o
What you reported is not what you did. It appears that grompp, gtraj, and
g_dist report the same value.
Please also report the value that you get from your pullx.xvg file that you get
from mdrun, which I suspect
will also be the same.
The difference that you report is actually between the first
Hi Chris,
and thank you for your reply. I should have included my g_dist command in
my first mail. Here goes:
I first run trjconv to extract the individual frames from my pulling
trajectory
$ trjconv -f pull.xtc -s pull.tpr -o conf.gro -sep -pbc mol -ur compact
Then, g_dist like so:
$ g_dist -s
Dear Gromacs users,
a while ago I have sent out a message regarding different distance measurements
in the pull code vs. those made by g_dist. Thanks to everybody who responded
and observed the same problem. I am still somewhat puzzled. Several users
suggested that this is connected to the 'sig
Hi, In the output pmf that you get from wham, do you have negative distances?
You mentioned your reaction coordinate ranges from -2 to 2 and your pullx
files have negative distances but from what I have observed, wham takes only
the magnitude of the distances and I presume your wham output will ran
As Bogdan suggested this could be an issue with the sign of the distance.
When you run grompp you get
>Pull group natoms pbc atom distance at start reference at t=0
> 0 994 497
> 1 2 46347 1.224 1.950
which suggests your startin
the positive number
should be in the calculations used inside WHAM.
Grüess
Stephan
Original-Nachricht
> Datum: Mon, 25 Jun 2012 02:32:40 -0700 (PDT)
> Von: anaome
> An: gmx-users@gromacs.org
> Betreff: [gmx-users] Re: umbrella sampling with distances larg
Thanks Stephan for your suggestions,
A finally found a solution for distance larger than half the box size:
1) Regenerate the tpr files with pbc=no
2) Perform WHAM analysis with the umbrella forces (-if)
--
View this message in context:
http://gromacs.5086.n6.nabble.com/umbrella-sampling-with-d
Steven Neumann wrote:
Dear Gmx Users, Dear Justin,
I run Umbrella Sampling for my ligand pulling using Justin's
Tutorial. Please, see attached my histogram and PMF profile.
I know it requires more sampling around distance from 0.8 to 2.5 nm.
1) Will more sampling affect the final deltaG wh
Thank you Justin, I will read it for sure and come back to my simulations!
Steven
On Thu, Nov 17, 2011 at 1:25 PM, Justin A. Lemkul wrote:
>
>
> Steven Neumann wrote:
>
>> Hi Justin,
>> I am sorry for so many questions but I do not understand something.
>> First we run the simulation of pullin
Steven Neumann wrote:
Hi Justin,
I am sorry for so many questions but I do not understand something.
First we run the simulation of pulling Chain A from ChainB with constant
force (pull_k1=1000) and constant velocity of pulling (pull_rate1=0.01)
We extract windows as we discussed and then r
Hi Justin,
I am sorry for so many questions but I do not understand something.
First we run the simulation of pulling Chain A from ChainB with constant
force (pull_k1=1000) and constant velocity of pulling (pull_rate1=0.01) We
extract windows as we discussed and then run simulations with those
con
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Re: umbrella sampling with "pull=constraint"
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID: <4eb7f727.3000...@vt.edu <mailto:4eb7f727.3000...
sampling windows? this observation is from last 10ns of 20ns
simulation.
>
> Message: 3
> Date: Mon, 07 Nov 2011 10:20:07 -0500
> From: "Justin A. Lemkul"
> Subject: Re: [gmx-users] Re: umbrella sampling with "pull=constraint"
> To: Discussion list for GROMA
Vijayaraj wrote:
and also I tried to plot the PMF curve from this data, I got few warning
messages like "no data point in bin 20, You may not get a reasonable
profile. Check your histograms!". the histogram shows poor sampling from
0.6 nm to 0.7 nm, and the windows in this position completely
and also I tried to plot the PMF curve from this data, I got few warning
messages like "no data point in bin 20, You may not get a reasonable
profile. Check your histograms!". the histogram shows poor sampling from
0.6 nm to 0.7 nm, and the windows in this position completely overlaps at
0.5-0.6 nm
Hello,
Thanks for the suggestions. I did umbrella simulation for 20ns and the pull
force is as below.
19960.-6.78192
19962.33.3579
19964.-3.1808
19966.-15.0304
19968.-55.4436
19970.-38.9422
19972.-9.41927
19974.-5.95981
19976.
Hi Justin,
Here is my complete code for umbrella sampling
title = Umbrella pulling simulation
define = -DPOSRES_2
integrator = md
dt = 0.002
tinit = 0
nsteps = 250 ; 5 ns
nstcomm = 10
nstxout = 5 ; every 100 ps
nstvout = 5
nstfout
DeChang Li wrote:
Message: 6
Date: Tue, 19 Oct 2010 09:30:47 -0400
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Umbrella sampling with temperature and
pressurecoupling method problem
To: Discussion list for GROMACS users ma
> Message: 6
> Date: Tue, 19 Oct 2010 09:30:47 -0400
> From: "Justin A. Lemkul"
> Subject: Re: [gmx-users] Umbrella sampling with temperature and
>pressurecoupling method problem
> To: Discussion list for GROMACS users
> Message-ID: <4cbd9d87.6080...@vt.edu>
> Content-Type: text/p
2008/8/4 Vitaly Chaban <[EMAIL PROTECTED]>
> Hi Alexandr,
>
> Have you thoroughly examined this thread as for using umbrella sampling:
> http://www.gromacs.org/pipermail/gmx-users/2005-December/018615.html ?
>
>
> --
> Vitaly V. Chaban
> School of Chemistry
> National University of Kharkiv
> Svobo
Hi Alexandr,
Have you thoroughly examined this thread as for using umbrella sampling:
http://www.gromacs.org/pipermail/gmx-users/2005-December/018615.html ?
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
sky
I am attempting to pull a ligand through a channel protein. I have setup the
umbrella sampling code and it seems to be working just fine except I get
large jumps in the
deviation of each pulled group from its restrained position at 1 ps
intervals. I am pulling three groups all relative to the backb
>
> is this perchance a bug or am i doing something
> wrong?
>
sorry, i rtfm.
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