On 11/10/13 9:14 AM, shahab shariati wrote:
Dear Justin
Very thanks for your reply.
What you described earlier should not be attempted with "distance"
geometry. It won't work very well. The use of restraints is almost
NEVER necessary, especially in the case where the reference group > is
mu
Dear Justin
Very thanks for your reply.
> What you described earlier should not be attempted with "distance"
> geometry. It won't work very well. The use of restraints is almost
> NEVER necessary, especially in the case where the reference group > is
much more massive than the pulling group.
I w
On 11/10/13 5:31 AM, shahab shariati wrote:
Dear Justin
Thanks for your reply.
You are right. I should not extrapolate too literally from your tutorial
to my system.
But, I have a general question:
There is 2 groups in COM pulling method (reference group + pull group).
If I want to use pu
Dear Justin
Thanks for your reply.
You are right. I should not extrapolate too literally from your tutorial
to my system.
But, I have a general question:
There is 2 groups in COM pulling method (reference group + pull group).
If I want to use pull_geometry = distance, so, I should fix referen
On 11/9/13 9:38 AM, shahab shariati wrote:
Dear Justin
Thanks for your explanation.
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.
Box vector alon
Dear Justin
Thanks for your explanation.
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.
Box vector along which the pulling is being conducted is Z.
1
On 11/9/13 8:22 AM, shahab shariati wrote:
Daer Justin
I studied your tutorial (Umbrella Sampling). It is very beneficial for me.
The system you considered was the dissociation of a single peptide from the
growing end of an protofibril.
You considered following parameters:
Chain_B: referenc
Daer Justin
I studied your tutorial (Umbrella Sampling). It is very beneficial for me.
The system you considered was the dissociation of a single peptide from the
growing end of an protofibril.
You considered following parameters:
Chain_B: reference group for pulling.
Chain_A: group to which pu
n list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling using pull codes
On 9/12/13 10:18 PM, mjyang wrote:
Dear Justin,
Thanks for your reply. I checked the content in pullx.xvg file as follows:
# GRowing Old MAkes el Chrono Sweat
#
s.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin Lemkul [jalem...@vt.edu]
Sent: Friday, September 13, 2013 10:33 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling using pull codes
On 9/12/13 10:18 PM, mjyang wrote:
> Dear Justin,
>
> Thanks for yo
On 9/12/13 10:18 PM, mjyang wrote:
Dear Justin,
Thanks for your reply. I checked the content in pullx.xvg file as follows:
# GRowing Old MAkes el Chrono Sweat
#
@title "Pull COM"
@xaxis label "Time (ps)"
@yaxis label "Posit
.org] On Behalf
Of Justin Lemkul [jalem...@vt.edu]
Sent: Thursday, September 12, 2013 10:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling using pull codes
On 9/12/13 9:55 AM, mjyang wrote:
> Dear GMX users,
>
> I'd like to perform the um
On 9/12/13 9:55 AM, mjyang wrote:
Dear GMX users,
I'd like to perform the umbrella sampling using the pull codes in gromacs.
The reaction coordinate is defined as the distance between the center of mass
(DCOM) of two domains in a protein. The following script is used:
---
Dear GMX users,
I'd like to perform the umbrella sampling using the pull codes in gromacs.
The reaction coordinate is defined as the distance between the center of mass
(DCOM) of two domains in a protein. The following script is used:
--- only for pull section
; Pull code
pull
Hi Po-chia,
On Sep 10, 2013, at 9:53 AM, "Chen, Po-chia" wrote:
> Hi all,
> I can't seem to find the correct combination of EDI parameters impose a
> harmonically-constrained simulation along an eigenvector in GROMACS 4.6.2,
> and I'd like to confirm that the inputs I have are actually correct
Hi all,
I can't seem to find the correct combination of EDI parameters impose a
harmonically-constrained simulation along an eigenvector in GROMACS 4.6.2, and
I'd like to confirm that the inputs I have are actually correct. Here is the
make_edi command I used to generate the .edi file fed to m
On 9/1/13 1:39 AM, Shima Arasteh wrote:
Hi,
I ran US on an ion through a channel inserted in a bilayer.
I used g_wham and got the profile output. In the visualized profile, I see a
region that the plot shows a flat line and it seems the data is missed there.
Would you please let me know wh
Hi,
I ran US on an ion through a channel inserted in a bilayer.
I used g_wham and got the profile output. In the visualized profile, I see a
region that the plot shows a flat line and it seems the data is missed there.
Would you please let me know what the reason of missing data is?
Thanks
Thanks Justin, Stephan. I am running both and will post my observations soon.
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Umbrella-sampling-position-restraints-tp5010405p5010422.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mail
. August 2013 um 21:57 Uhr
Von: rookie417
An: gmx-users@gromacs.org
Betreff: [gmx-users] Umbrella sampling - position restraints
Dear GROMACS users,
I followed the Umbrella Sampling tutorial to run a simple simulation of
pulling polymer chain from the surface of micelle. I used position
restraints
On 8/8/13 3:57 PM, rookie417 wrote:
Dear GROMACS users,
I followed the Umbrella Sampling tutorial to run a simple simulation of
pulling polymer chain from the surface of micelle. I used position
restraints for the initial equilibration, however I realized a typo in the
define=-DPOSRES mdp file
Dear GROMACS users,
I followed the Umbrella Sampling tutorial to run a simple simulation of
pulling polymer chain from the surface of micelle. I used position
restraints for the initial equilibration, however I realized a typo in the
define=-DPOSRES mdp files for pulling, US_NPT and US_MD simulati
endet: Mittwoch, 31. Juli 2013 um 12:46 Uhr
Von: "Steven Neumann"
An: "Discussion list for GROMACS users"
Betreff: Re: [gmx-users] Umbrella Sampling
They do not dissociate...Are you sure? My mdp specifies only ligand as a
pull_group1. I think it would change having ions in this grou
On 7/31/13 10:19 AM, Mohsen Ramezanpour wrote:
Dear Dr.Justin
I read that article, It was very helpful. Thanks a lot.
After using g_wham with bootstrapping options.
I have got an averaged PMF profile (like Fig.2C in that article) and
an standard deviation (like Fig.2D In that article) which ob
Dear Dr.Justin
I read that article, It was very helpful. Thanks a lot.
After using g_wham with bootstrapping options.
I have got an averaged PMF profile (like Fig.2C in that article) and
an standard deviation (like Fig.2D In that article) which obtained in
this way.
As you see, the standard deviat
;
>> -Justin
>>
>>
>>>> On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs
>>>> wrote:
>>>>
>>>>
>>>>> will get the PMF profile for my
>>>>>> ligand binding or ligand and two ions binding?
>>>>>&
;>>>> ligand binding or ligand and two ions binding?
>>>>>
>>>>
>>>> It would be the ligand and two ions unless the ions also at some point
>>>> discossiate from the ligand once in solvent. Could add positional
>>>> restrain
unless the ions also at some point
discossiate from the ligand once in solvent. Could add positional restraint
for them, but dont know how that effects the calculation?
*Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr
*Von:* "Steven Neumann"
*An:* "Discussion list for GROMACS users&q
Thank you for your reply Dr. Justin
On 7/31/13, Justin Lemkul wrote:
>
>
> On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote:
>> Hi everyone
>>
>> How can we have an error estimation for Gibbs binding free energy when
>> I do umbrella sampling and PMF profile?
>>
>> Actually I did an umbrella sampling
On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote:
Hi everyone
How can we have an error estimation for Gibbs binding free energy when
I do umbrella sampling and PMF profile?
Actually I did an umbrella sampling for protein and ligand complex and
I have a PMF profile now but I do not know how much i
Hi everyone
How can we have an error estimation for Gibbs binding free energy when
I do umbrella sampling and PMF profile?
Actually I did an umbrella sampling for protein and ligand complex and
I have a PMF profile now but I do not know how much is my error!
Thanks in advance for any suggestion
t;Steven Neumann"
>> *An:* "Discussion list for GROMACS users"
>> *Betreff:* [gmx-users] Umbrella Sampling
>> Dear Gmx Users,
>>
>> I run SMD to extract the windows for US calculations. The system involves
>> negatively charged ligand and protein.
t; *Von:* "Steven Neumann"
> *An:* "Discussion list for GROMACS users"
> *Betreff:* [gmx-users] Umbrella Sampling
> Dear Gmx Users,
>
> I run SMD to extract the windows for US calculations. The system involves
> negatively charged ligand and protein. I generated the pro
lation?
Gesendet: Mittwoch, 31. Juli 2013 um 09:29 Uhr
Von: "Steven Neumann"
An: "Discussion list for GROMACS users"
Betreff: [gmx-users] Umbrella Sampling
Dear Gmx Users,
I run SMD to extract the windows for US calculations. The system involves
negatively charged ligand an
Dear Gmx Users,
I run SMD to extract the windows for US calculations. The system involves
negatively charged ligand and protein. I generated the protein-ligand
complex within self assembly MD simulations.
I pulled my molecule away and two ions were also detached from the protein
surface being att
Please remember to keep the discussion on the list.
On 7/26/13 12:04 PM, Shima Arasteh wrote:
what I aim to see is that the pulled ion should be remained in center of the
channel (peptide inserted in lipid bilayer).
I didn't restrain the channel, it makes a little bit hard for me to judge
exa
On 7/26/13 11:52 AM, Shima Arasteh wrote:
Thanks for your previous replies. All are always beneficial and I appreciate
you.
As I see in pullx.xvg file, the third column refers to the distance of pull
group and reference group. All around -1.2. Is it sufficient to judge that the
US has bee
suggestions in advance.
Sincerely,
Shima
- Forwarded Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Sent: Thursday, July 25, 2013 4:25 PM
Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion
On 7/25/13 7:52 AM, Shima Arasteh wrote:
> After running for 100 ps
= com
Would you please let me know your suggestions ?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh
Cc:
Sent: Wednesday, July 24, 2013 9:41 PM
Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion
On 7/24/13 11:53 AM, Shima Arasteh wrote:
Yes
know your suggestions ?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh
Cc:
Sent: Wednesday, July 24, 2013 9:41 PM
Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion
On 7/24/13 11:53 AM, Shima Arasteh wrote:
> Yes, Thanks.
>
> Would you
odd result for npt_US or md_US?
Many many thanks for your time and suggestions.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Wednesday, July 24, 2013 8:05 PM
Subject: Re: [gmx-users] Umbrella Sampling _ pulle
On 7/24/13 11:30 AM, Shima Arasteh wrote:
Hi,
I am trying to run US on a system composed of lipid bilayer/ ion/ water/
peptide. The peptide is inserted through the lipid bilayer and I' d like to
study the ion conduction through the peptide across the membrane.
In order to do so, I tried to
Hi,
I am trying to run US on a system composed of lipid bilayer/ ion/ water/
peptide. The peptide is inserted through the lipid bilayer and I' d like to
study the ion conduction through the peptide across the membrane.
In order to do so, I tried to set a specific ion ( Ces with the atom number
[gmx-users] Umbrella Sampling settings
On 7/12/13 11:32 AM, Shima Arasteh wrote:
>
>
>
> Allright.
> As I said earlier, my system is a lipid bilayer. A channel is inserted in it
> and I want to run US on this system.
> An ion is considered in center of the each window, the rea
On 7/12/13 11:32 AM, Shima Arasteh wrote:
Allright.
As I said earlier, my system is a lipid bilayer. A channel is inserted in it
and I want to run US on this system.
An ion is considered in center of the each window, the reaction coordinate is
set to z, so the group which is pulled is an
group?
Would you please give me any suggestions?
Thanks for all your time and consideration.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Friday, July 12, 2013 1:41 AM
Subject: Re: [gmx-users] Umbrella Sampling settings
On
group?
Would you please give me any suggestions?
Thanks for all your time and consideration.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Friday, July 12, 2013 1:41 AM
Subject: Re: [gmx-users] Umbrella Sampling settings
On 7/
ima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS users
Cc:
Sent: Friday, July 12, 2013 1:37 AM
Subject: Re: [gmx-users] Umbrella Sampling settings
On 7/11/13 4:21 PM, Shima Arasteh wrote:
Hi,
I want to run Umbrella Sampling on m
013 1:37 AM
Subject: Re: [gmx-users] Umbrella Sampling settings
On 7/11/13 4:21 PM, Shima Arasteh wrote:
> Hi,
>
> I want to run Umbrella Sampling on my system. In initial configurations, an
> ion is located in center of the window.
> Some mdp file settings for running US, as I
On 7/11/13 4:21 PM, Shima Arasteh wrote:
Hi,
I want to run Umbrella Sampling on my system. In initial configurations, an ion
is located in center of the window.
Some mdp file settings for running US, as I found in US tutorial are :
; Pull code
pull= umbrella
pull_geometry = dist
Hi,
I want to run Umbrella Sampling on my system. In initial configurations, an ion
is located in center of the window.
Some mdp file settings for running US, as I found in US tutorial are :
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start
On 7/9/13 7:38 PM, rookie417 wrote:
Thanks Justin and Stephan,
One more question, while pulling from the interior of a multiple monomer
micelle structure, I used higher force constants (5000 kJ/mol/nm^2) for
position restraints on the reference group to keep the system intact. I am
assuming t
Thanks Justin and Stephan,
One more question, while pulling from the interior of a multiple monomer
micelle structure, I used higher force constants (5000 kJ/mol/nm^2) for
position restraints on the reference group to keep the system intact. I am
assuming that I have to use different pull_k1 for
users@gromacs.org
Betreff: [gmx-users] Umbrella sampling- force vs time plots
Hello all,
I am trying to understand the force vs time plots using Gromacs' umbrella
sampling method. I am trying to pull a short polymer chain from the interior
of a micelle and see what the PMF looks like. I use the
On 7/9/13 12:56 PM, rookie417 wrote:
Hello all,
I am trying to understand the force vs time plots using Gromacs' umbrella
sampling method. I am trying to pull a short polymer chain from the interior
of a micelle and see what the PMF looks like. I use the following parameters
to run the pulling
Hello all,
I am trying to understand the force vs time plots using Gromacs' umbrella
sampling method. I am trying to pull a short polymer chain from the interior
of a micelle and see what the PMF looks like. I use the following parameters
to run the pulling simulation for 500ps to pull the polymer
Great, thanks! I'll give it a try.
On 7/8/13 1:02 PM, Justin Lemkul wrote:
On 7/8/13 12:58 PM, Justin Lemkul wrote:
On 7/8/13 12:56 PM, Diana Fusco wrote:
Hi Justin,
I have actually followed your tutorial to perform umbrella sampling
on CPU and
it worked great. Can I use the same file fo
On 7/8/13 12:58 PM, Justin Lemkul wrote:
On 7/8/13 12:56 PM, Diana Fusco wrote:
Hi Justin,
I have actually followed your tutorial to perform umbrella sampling on CPU and
it worked great. Can I use the same file for GPU acceleration or I have to add
some fields and commands?
There's nothi
On 7/8/13 12:56 PM, Diana Fusco wrote:
Hi Justin,
I have actually followed your tutorial to perform umbrella sampling on CPU and
it worked great. Can I use the same file for GPU acceleration or I have to add
some fields and commands?
There's nothing GPU-specific in the .mdp file.
-Justin
Hi Justin,
I have actually followed your tutorial to perform umbrella sampling on
CPU and it worked great. Can I use the same file for GPU acceleration or
I have to add some fields and commands?
Thanks!
Diana
On 7/8/13 12:47 PM, Justin Lemkul wrote:
On 7/8/13 12:08 PM, Diana Fusco wrote:
On 7/8/13 12:08 PM, Diana Fusco wrote:
Hello,
I'd like to know if it is possible with Gromacs 4.6 to perform umbrella sampling
using GPU with orientational restraints. If it is, can you give me a simple
example of mdp file to see how it works?
As to whether or not it works, mdrun will compl
Hello,
I'd like to know if it is possible with Gromacs 4.6 to perform umbrella
sampling using GPU with orientational restraints. If it is, can you give
me a simple example of mdp file to see how it works?
Thanks
Diana
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org
It's just the xvv file. g_wham uses the letter 'z' to denote the reaction
coordinate.
Erik
On 2 Jul 2013, at 11:32, battis...@libero.it wrote:
>
>
>
>
>
>
> Dear users and experts
>
> I'm doing an umbrella-samplig calculation to obtain the PMF when two
> structure (A and B) are at vario
Dear users and experts
I'm doing an umbrella-samplig calculation to obtain the PMF when two structure
(A and B) are at various X distances.
I setted my md-umbrella.mdp file as in follows:
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = umbr
Thanks Erik
On 06/12/2013 01:50 PM, Erik Marklund wrote:
Hi,
No, I'm afraid not. pull-dim not only determines what components are to be
printed, it also determines in what dimensions the force is to be applied
during the simulation.
Erik
On 12 Jun 2013, at 13:32, Kenny Bravo Rodriguez
wro
Hi,
No, I'm afraid not. pull-dim not only determines what components are to be
printed, it also determines in what dimensions the force is to be applied
during the simulation.
Erik
On 12 Jun 2013, at 13:32, Kenny Bravo Rodriguez
wrote:
> Dear Gromacs Users,
>
> I runned and Umbrella Sampli
Dear Gromacs Users,
I runned and Umbrella Sampling simulation but I made a mistake in the
value of the pull_dim option, so gromacs printed the z component of the
force instead of the x component that i need (with the option -pf of
mdrun). I have all files from the simulation.
Is there a way to
hr
> *Von:* "gromacs query"
> *An:* "Discussion list for GROMACS users"
> *Betreff:* [gmx-users] umbrella sampling for two polymer interaction
> Dear All,
>
> I want to do Umbrella sampling between two different polymers (A and B)
> interacting with each othe
Dear Jiom,
Look at justines tutorial, there's example pull .mdp.
Stephan Watkins
Gesendet: Donnerstag, 30. Mai 2013 um 14:44 Uhr
Von: "gromacs query"
An: "Discussion list for GROMACS users"
Betreff: [gmx-users] umbrella sampling for two polymer interaction
Dear All,
I want to do Umbrella sampling between two different polymers (A and B)
interacting with each other with starting configuration separated by some
distance and I am trying to bring them closer.
I have some queries regarding pull inputs: (this is for to run a umbrella
sampling at some dis
HI,
I would like to compute an umbrella sampling simulation for o protein
divided in two domain, with Center of mass pulling using as constraint
between the two domains. And the constraint is applied instead of a
harmonic potential
I create a pull.mdp file with this option for the pull:
title
On 4/29/13 6:42 AM, Shima Arasteh wrote:
Dear Justin,
About Umbrella sampling tutorial, would you please let me know why you created
an index file contains of chain A and chain B?
Also, what's the meaning of 19 and 20 created by a text editoras groups.txt
file? I can not understand this.
Dear Justin,
About Umbrella sampling tutorial, would you please let me know why you created
an index file contains of chain A and chain B?
Also, what's the meaning of 19 and 20 created by a text editoras groups.txt
file? I can not understand this.
Thanks in advance.
Sincerely,
Shima
--
Look for
pull_geometry = direction_periodic
This should solve the problem.
Greetings
Thomas
Am 20.03.2013 12:00, schrieb gmx-users-requ...@gromacs.org:
Dear all,
I want to use Umbrella sampling method to calculate the potential of
mean force. Unfortunately, the distance of my two groups is ve
Dear Justin,
Thank you very much for your quick reply.
Regards,
Ramesh.
On Wed, Jan 2, 2013 at 10:24 AM, Justin Lemkul wrote:
>
>
> On 1/1/13 11:48 PM, ramesh cheerla wrote:
>
>> Dear Gromacs users,
>>
>> I am performing umbrella samplin
On 1/1/13 11:48 PM, ramesh cheerla wrote:
Dear Gromacs users,
I am performing umbrella sampling
simulations by selecting configurations with spacing window of 0.02nm from
pulling simulations with the following options in .mdp file to get PMF
along a axis
On 12/12/12 5:26 PM, Justin Lemkul wrote:
On 12/12/12 5:15 PM, Davide Mercadante wrote:
Dear Justin,
Thank you for your reply. To be sure I carefully ran the simulations again
using the following .mdp file that includes the pull lines and
-DPOSRES_B to restrain chain B from being pulled whe
On 12/12/12 5:15 PM, Davide Mercadante wrote:
Dear Justin,
Thank you for your reply. To be sure I carefully ran the simulations again
using the following .mdp file that includes the pull lines and
-DPOSRES_B to restrain chain B from being pulled when chain A is being
pulled (it is the .mdp fil
Dear Justin,
Thank you for your reply. To be sure I carefully ran the simulations again
using the following .mdp file that includes the pull lines and
-DPOSRES_B to restrain chain B from being pulled when chain A is being
pulled (it is the .mdp file given in the tutorial):
title = Umbrella
On 12/11/12 2:40 AM, Davide Mercadante wrote:
Dear Justin,
I have been practicing umbrella sampling simulations following your tutorial
step by step. I have just finished to perform the pull simulations to
identify the configurations to use in the umbrella runs. I have used the
distances.pl sc
Dear Justin,
I have been practicing umbrella sampling simulations following your tutorial
step by step. I have just finished to perform the pull simulations to
identify the configurations to use in the umbrella runs. I have used the
distances.pl script to run iteratively g_dist and the resulting f
Dear Justin,
I am very thankful to you for your reply, you are correct, I have plotted
the histo.xvg file in wrong manner. After plotting histograms in correct
manner I have realized that my sampling is very poor as histograms and
there overlapping is restricted to some regions only, no histogram
On 11/26/12 1:03 AM, ramesh cheerla wrote:
Dear Gromacs users,
I am calculating PMF for the ion permeation through a tunnel, using
umbrella sampling. In my system I have some binding sites with ions, I have
removed some ions from binding sites before pulling and In pulling
simulations
Can you please let us know exactly how you got the two values that you find to
be different (but expected
to be the same)? i.e. post your full g_dist command and explain how you
observed the value in the output from
mdrun. One frame should be enough for now (as long as you are sure -- and can
pr
current Gromacs to do it.
-Jianguo
From: Netaly Khazanov
To: gmx-users@gromacs.org
Sent: Wednesday, 17 October 2012, 16:47
Subject: [gmx-users] Umbrella sampling after TMD of NAMD
Dear All,
I've performed TMD simulation using NAMDprogram. I'd like to cal
On 10/17/12 9:17 AM, Netaly Khazanov wrote:
Thanks.
However, I can restrain the position of backbone (x,y,z -coordinates) while
running umbrella sampling and treat it like reaction coordinate. Is it
right?
Maybe I am missing something.
pull = umbrella
pull_geometry = position
;pull_dim = Y
Thanks.
However, I can restrain the position of backbone (x,y,z -coordinates) while
running umbrella sampling and treat it like reaction coordinate. Is it
right?
Maybe I am missing something.
pull = umbrella
pull_geometry = position
;pull_dim = Y Y Y
pull_start = yes
pull_ngroups = 1
;pull_grou
On 10/17/12 5:44 AM, Netaly Khazanov wrote:
Of course I read Justin's tutorial.
The reason I am asking is that I am not sure how to do it.
As far as I am aware, there is no way to conduct umbrella sampling in this way
using Gromacs. The PMF calculations that Gromacs does are based on restr
Of course I read Justin's tutorial.
The reason I am asking is that I am not sure how to do it.
On Wed, Oct 17, 2012 at 11:09 AM, Arman Mahboubi Soufiani <
armansoufi...@gmail.com> wrote:
> Hi,
>
> I recommend you Justin's tutorial on Umbrella Sampling
>
> http://www.bevanlab.biochem.vt.edu/Pages/
Hi,
I recommend you Justin's tutorial on Umbrella Sampling
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
Regards
Arman
On Wed, Oct 17, 2012 at 10:47 AM, Netaly Khazanov wrote:
> Dear All,
>
> I've performed TMD simulation using NAMDprogram. I'd lik
Dear All,
I've performed TMD simulation using NAMDprogram. I'd like to calculate PMF
plot based on the frames that were taken from TMD simulations by using
GROMACS.
The coordinate of reaction is RMSD of backbone.
The first step is to do Umbrella sampling. The question is how fix the
position of
Hello Gromacs users,
The solution that ended up working is selecting a different pull_pbcatom0
from the reference group, the protein, such that the atom is approx. in the
center of mass of the protein.
I hope that others may find this useful,
Thanks to Martin Vesper and Justin Lemkul for their i
On 9/28/12 2:19 PM, Archana Sonawani wrote:
Dear Justin,
So do I have to carry out umbrella sampling simulations separately for the
three complexes or put the three ligands together with the protein and pull
the ligands one by one to calculate the binding energy. I am confused.
Each complex
Dear Justin,
So do I have to carry out umbrella sampling simulations separately for the
three complexes or put the three ligands together with the protein and pull
the ligands one by one to calculate the binding energy. I am confused.
Thanks in advance.
Regards,
Archana
On Fri, Sep 28, 2012 at
On 9/28/12 9:27 AM, Archana Sonawani wrote:
Hi,
I have performed simulations for 3 different ligands complexed with the
same protein. I want to compare the binding energies of these different
three complexes. Will umbrella sampling be useful in this case?
Several methods could be used, and
Thank you all for your help,
Sheeba-
Yes, I get both positive and negative results. I think what you describe is
what I would get if I used 'distance' for the geometry.
In any case, I have values from +2 to about -3, and they are not evenly
distributed (unlike the coordinates, which are more or le
On 9/10/12 9:30 PM, Jianguo Li wrote:
I guess is that g_wham takes the distance from tpr file which calculates the
distance using grommp.
It seems that the distances calculated using g_dist and grompp are different,
as discussed in this forum about 10 days ago.
This is a fairly frequent c
: Discussion list for GROMACS users
Cc:
Sent: Monday, 10 September 2012, 23:54
Subject: Re: [gmx-users] umbrella sampling (PMF) position discrepancy
Hi Justin, thank you for you quick reply.
On Mon, Sep 10, 2012 at 6:41 PM, Justin Lemkul wrote:
>
>
> On 9/10/12 11:22 AM, Raphael Alhad
Hi Justin, thank you for you quick reply.
On Mon, Sep 10, 2012 at 6:41 PM, Justin Lemkul wrote:
>
>
> On 9/10/12 11:22 AM, Raphael Alhadeff wrote:
>
>> Dear Gromacs users,
>>
>> I've been trying to run an umbrella sampling (for the purpose of pmf)
>> using
>> Gromacs 4.5.5.
>> My system consists
On 9/10/12 11:22 AM, Raphael Alhadeff wrote:
Dear Gromacs users,
I've been trying to run an umbrella sampling (for the purpose of pmf) using
Gromacs 4.5.5.
My system consists of a membrane protein transporter and a Na ion passing
through it, from the water bulk on one side of the membrane to t
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