On 7/6/18 10:42 AM, hosein geraili wrote:
Dear all,
I have a question regarding the umbrella sampling tutorial. I am using the bash script to
create the summary_distances.dat, but the problem is at first I would get the error
"Unknown command-line option -o", then I used -oh instead of -o
Dear all,
I have a question regarding the umbrella sampling tutorial. I am using the bash
script to create the summary_distances.dat, but the problem is at first I would
get the error "Unknown command-line option -o", then I used -oh instead of -o
which worked, but the problem is the
On 11/10/16 10:46 AM, Lindsay, Richard J. wrote:
Hi,
I am attempting to follow the gromacs umbrella sampling tutorial but have run
into an issue at the data analysis step.
When I run the gmx wham command I get only one histogram, even though I
collected 24 umbrella trajectories.
You're
Hi,
I am attempting to follow the gromacs umbrella sampling tutorial but have run
into an issue at the data analysis step.
When I run the gmx wham command I get only one histogram, even though I
collected 24 umbrella trajectories.
Here is the command I am running:
gmx wham -it tpr-files.dat
Any idea on this topic?
Thanks
> On 07 Oct 2016, at 14:13, gozde ergin wrote:
>
> Thanks Justin.
> I want infinite dilute bulk that’s why I do not want any surfactant molecule
> inside the bulk.
> I may put a ‘’wall’’ just below the surface molecules in order to inhibit
Thanks Justin.
I want infinite dilute bulk that’s why I do not want any surfactant molecule
inside the bulk.
I may put a ‘’wall’’ just below the surface molecules in order to inhibit their
travel to bulk but I do not know how to remove this effect from PMF.
> On 07 Oct 2016, at 13:40, Justin
On 10/7/16 4:41 AM, gozde ergin wrote:
Dear all,
I would like to ask a question about Justin’s tutorial. By using the
POSRES_B, a restraint is applied on chain B in order to immobile it. Is the
effect of this restraint removed during the WHAM?
Not to my knowledge, no. The restraints in
Dear all,
I would like to ask a question about Justin’s tutorial.
By using the POSRES_B, a restraint is applied on chain B in order to immobile
it. Is the effect of this restraint removed during the WHAM?
I want to do a similar thing by applying restraint force on the organic
molecule on the
On 6/7/16 3:13 AM, amitbe...@chemeng.iisc.ernet.in wrote:
Hello,
I was running the simulation for the umbrella sampling tutorial by Dr.
Justin Lemkul in GROMACS 5.1.2 and I followed the steps exactly as they
were mentioned.
But in my summary_distances.dat there is one column. the COM column is
Hello,
I was running the simulation for the umbrella sampling tutorial by Dr.
Justin Lemkul in GROMACS 5.1.2 and I followed the steps exactly as they
were mentioned.
But in my summary_distances.dat there is one column. the COM column is
missing. I am new to gromacs . So please help me out.
Hello everyone
I am following the Justin Lemkul's tutorial for Umbrella sampling:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
I am at the step where i want to perfom the NPT equilibration. Using the
input file provided in the tutorial, I use
March 2015 9:45 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial
On 3/17/15 9:06 PM, Ming Tang wrote:
Hi Justin,
Thanks a lot. I can move forward now.
Recently, I am trying to pull a triple helix, and want to fix the center of
mass of the three terminal atoms
On 4/7/15 7:11 AM, Ming Tang wrote:
Hi, Justin
I am working with a triple helix using umbrella sampling method. When
generating configurations, I pulled 1ns (md_pull.mdp). Then I got 15
configurations using 0.03 spacing. They are conf0.gro conf5.gro conf10.gro
conf15.gro conf17.gro conf18.gro
On 3/17/15 9:06 PM, Ming Tang wrote:
Hi Justin,
Thanks a lot. I can move forward now.
Recently, I am trying to pull a triple helix, and want to fix the center of
mass of the three terminal atoms. One paper said that it can be done by means
of a strong harmonic restrain with a super large
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: Monday, 16 March 2015 9:27 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial
On 3/15/15 9:57 PM, Ming Tang wrote:
Dear Justin,
I have tried many cases, and only your code runs smoothly
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: Monday, 16 March 2015 9:27 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial
On 3/15/15 9:57 PM
...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial
On 3/17/15 8:08 PM, Ming Tang wrote:
Hi Justin,
Here is the error message.
tm@tm-HP-Z420-Workstation:~/umbrella$ perl distances.pl Bareword found
where operator expected at distances.pl line 8, near gmx distance -n
...@maillist.sys.kth.se] On Behalf Of
Justin Lemkul
Sent: Monday, 16 March 2015 9:27 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial
On 3/15/15 9:57 PM, Ming Tang wrote:
Dear Justin,
I have tried many cases, and only your code runs smoothly. If I set
pull-ngroups = 1
...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming
Tang
Sent: Wednesday, 18 March 2015 8:14 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial
Yes, it can not run. But I can extract the COM of different conf.groone by one
manually
March 2015 8:14 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial
Yes, it can not run. But I can extract the COM of different conf.groone by one
manually. Due to the time difference, I will update the error message when I
get to the office.
Thanks.
Sent from my Huawei
On 3/15/15 9:57 PM, Ming Tang wrote:
Dear Justin,
I have tried many cases, and only your code runs smoothly. If I set
pull-ngroups = 1, it will warn that pull-group2-name= Chain_A has not been
defined.
The code you gave me last time runs well. Though the COM between Chain_A and
Chain_B
...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: Friday, 13 March 2015 10:57 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial
On 3/12/15 8:49 PM, Ming Tang wrote:
Dear Justin,
I switched Chain_A and Chain_B
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming
Tang
Sent: Thursday, 12 March 2015 11:34 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial
Hi Justin,
Your code works!
Thank you very much.
Regards,
Ming
-Original Message-
From
On 3/11/15 4:17 AM, Ming Tang wrote:
Dear all,
I was learning the Umbrella Sampling tutorial step by step on Gromacs 5.0.4.
Everything was fine until I got to the step five (run the continuous
pulling simulation).
Then I turned to the 5.0.4 manual, and tried to modify the pull code,
Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: Thursday, 12 March 2015 9:50 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial
On 3/12/15 2:41 AM, Ming
On 3/12/15 8:49 PM, Ming Tang wrote:
Dear Justin,
I switched Chain_A and Chain_B in the .mdp file, but got the same result.
In the tutorial:
pull-ngroups: (1)
The number of pull groups, not including the absolute reference group, when
used. And we need to assign the Chain_B as the reference
On 3/12/15 2:41 AM, Ming Tang wrote:
Dear Justin,
The results turned out that the COM distance between them is the same over
time, seems that both Chain_A and Chain_B had been pulled by the same force in
the same direction, which is different from the tutorial.
Switch Chain_A and
On 3/11/15 8:58 PM, Ming Tang wrote:
Dear Justin,
Thanks for your help.
I changed the group names to Chain_A and Chain_B in my index file, and modified
the COM pulling code.
; COM pulling
pull= umbrella
pull_geometry = distance ; simple distance increase
pull_dim= N N
On 3/11/15 4:17 AM, Ming Tang wrote:
Dear all,
I was learning the Umbrella Sampling tutorial step by step on Gromacs 5.0.4.
Everything was fine until I got to the step five (run the continuous pulling
simulation).
Then I turned to the 5.0.4 manual, and tried to modify the pull code, but
Dear all,
I was learning the Umbrella Sampling tutorial step by step on Gromacs 5.0.4.
Everything was fine until I got to the step five (run the continuous pulling
simulation).
Then I turned to the 5.0.4 manual, and tried to modify the pull code, but
failed.
; Pull code in tutorial
pull
...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial
On 3/11/15 8:58 PM, Ming Tang wrote:
Dear Justin,
Thanks for your help.
I changed the group names to Chain_A and Chain_B in my index file, and
modified the COM pulling code.
; COM pulling
pull= umbrella
pull_geometry
Hi Dear Gromacs Users
I am following umbrella sampling tutorial provided by Dr Justin Lemkul
(This tutorial is not updated for Gromacs 5 However I am using Gromacs
5.0.2 and i am trying my best to use files and commands compatible with
version 5)
I have done all the parts up to pulling section
Dear Users
Firstly thanks to Dr. Lemkul for his immensely informative and helpful
tutorials. I am following the umbrella sampling tutorial for one of my
projects.
During the placement of the molecule inside the box , the tutorial tells us
to visualize in VMD. Now , upon visualizing I find that
On 10/31/14 8:48 PM, Agnivo Gosai wrote:
Dear Users
Firstly thanks to Dr. Lemkul for his immensely informative and helpful
tutorials. I am following the umbrella sampling tutorial for one of my
projects.
During the placement of the molecule inside the box , the tutorial tells us
to visualize
Dear Users
I am following the Umbrella Sampling tutorial by Dr. Lemkul and would like
to have one of my doubts addressed :-
After using pdb2gmx on the supplied pdb file , a topology file is obtained
specifying the topology files for different protein chains in .itp format..
Inside the .itp files
Since the spring has a finite force constant, it is quite naturally that
one observes fluctuations in the distance (between reference and pulled
group) and forces.
Greetings
Thomas
Am 11.01.2014 22:45, schrieb
gromacs.org_gmx-users-requ...@maillist.sys.kth.se:
Hi,
Dear Gromacs Users
I was
On 1/11/14, 11:50 AM, Andres Ortega wrote:
Hi,
Dear Gromacs Users
I was running de Umbrella Sampling Tutorial, and when i get the frames from
the trajectory, there are some frames like this:
489 5.3776196
490 5.3817739
491 5.3752654
492 5.3619911
493 5.3890083
494
Dear Justin
Very thanks for your reply
I will slow pulling by changing pull_rate1 from 0.01 to 0.001
and pull_k1 from 1000 to 100.
I have a basic question. Before minimization, where should I put drug
molecule? into water molecules or into lipid bilayer? Should I put drug
molecule in the
On 12/1/13 8:04 AM, shahab shariati wrote:
Dear Justin
Very thanks for your reply
I will slow pulling by changing pull_rate1 from 0.01 to 0.001
and pull_k1 from 1000 to 100.
I have a basic question. Before minimization, where should I put drug
molecule? into water molecules or into lipid
Dear Justin
When I placed drug within the lipid bilayer, after Generating Configurations
step, I obtained 501 gro files. When I used distance.pl script for these
gro files, my summary_distances.dat file is as follows:
00.2756352
10.2535359
20.2447009
30.3004653
40.2936225
5
On 12/1/13 10:38 AM, shahab shariati wrote:
Dear Justin
When I placed drug within the lipid bilayer, after Generating Configurations
step, I obtained 501 gro files. When I used distance.pl script for these
gro files, my summary_distances.dat file is as follows:
00.2756352
10.2535359
The output you got indicates that the pulled group came to the
location where it is expected by gromacs to be.
The input looks correct, but gromacs' pull code is with surprise
inside. I would try to pull in opposite direction, i.e. pull_vec1 = -0
0 1. Turning off barostat during pulling also
Dear Justin
My system contains lipid bilayer + drug + water molecules.
I want to calculate Potential of mean force as a function of the
distance between the centers of mass of drug and the lipid bilayer.
Based on your suggestion I used pull_geometry = position for my case.
After the
On 11/30/13 9:22 AM, shahab shariati wrote:
Dear Justin
My system contains lipid bilayer + drug + water molecules.
I want to calculate Potential of mean force as a function of the
distance between the centers of mass of drug and the lipid bilayer.
Based on your suggestion I used
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