Re: [gmx-users] umbrella sampling tutorial

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 whi

[gmx-users] umbrella sampling tutorial

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 summary_dis

Re: [gmx-users] Umbrella sampling tutorial WHAM issue

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 p

[gmx-users] Umbrella sampling tutorial WHAM issue

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 -

Re: [gmx-users] Umbrella sampling tutorial

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 > their travel to bulk

Re: [gmx-users] Umbrella sampling tutorial

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 Le

Re: [gmx-users] Umbrella sampling tutorial

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 the

[gmx-users] Umbrella sampling tutorial

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 b

Re: [gmx-users] Umbrella sampling Tutorial by Dr. Lemkul

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

[gmx-users] Umbrella sampling Tutorial by Dr. Lemkul

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. Regards

Re: [gmx-users] Umbrella sampling tutorial - V-rescale or Berendsen thermostat

On 11/18/15 11:37 AM, Martin Nors Pedersen wrote: 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

[gmx-users] Umbrella sampling tutorial - V-rescale or Berendsen thermostat

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 gr

Re: [gmx-users] umbrella sampling tutorial

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

Re: [gmx-users] umbrella sampling tutorial

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

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. One paper said that it can be done by means of a strong harmonic restrain with a super large sp

Re: [gmx-users] umbrella sampling tutorial

mx-us...@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, ne

Re: [gmx-users] umbrella sampling tutorial

Thanks, Ming -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 Ming Tang Sent: Wednesday, 18 March 2015 8:14 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] umbrella sampling tutorial

Re: [gmx-users] umbrella sampling tutorial

istances.pl aborted due to compilation errors. Thanks, Ming -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 Ming Tang Sent: Wednesday, 18 March 2015 8:14 AM To: gmx-us...@gromacs.org Subject:

Re: [gmx-users] umbrella sampling tutorial

Regards, > Ming > > -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 > Sub

Re: [gmx-users] umbrella sampling tutorial

---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,

Re: [gmx-users] umbrella sampling tutorial

can run. Could you help to figure out this problem? Regards, Ming -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 Su

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, 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 rema

Re: [gmx-users] umbrella sampling tutorial

users-boun...@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 s

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 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 g

Re: [gmx-users] umbrella sampling tutorial

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

Re: [gmx-users] umbrella sampling tutorial

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 Chain_B

Re: [gmx-users] umbrella sampling tutorial

> 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 pul

Re: [gmx-users] umbrella sampling tutorial

[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

Re: [gmx-users] umbrella sampling tutorial

...@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 > pu

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 = distance ; simple distance increase pull_dim= N N

Re: [gmx-users] umbrella sampling tutorial

ject: Re: [gmx-users] umbrella sampling tutorial 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). >

Re: [gmx-users] umbrella sampling tutorial

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 fail

[gmx-users] umbrella sampling tutorial

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

[gmx-users] Umbrella sampling Tutorial Fatal Error

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 ver

Re: [gmx-users] Umbrella Sampling Tutorial Question

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 i

[gmx-users] Umbrella Sampling Tutorial Question

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 the

Re: [gmx-users] Umbrella Sampling tutorial by Dr. Justin Lemkul

On 10/26/14 4:32 PM, Agnivo Gosai wrote: 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 c

[gmx-users] Umbrella Sampling tutorial by Dr. Justin Lemkul

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

Re: [gmx-users] Umbrella Sampling Tutorial

Thanks ! Andrés Ortega Ing. Electrónica Universidad del Valle El 13/01/2014, a las 8:59, "Thomas Schlesier" escribió: > 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.

[gmx-users] Umbrella Sampling Tutorial

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

Re: [gmx-users] Umbrella Sampling Tutorial

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 5.3

[gmx-users] Umbrella Sampling Tutorial

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 5.3918220 495 5.4115819 496 5.4074620 497

Re: [gmx-users] Umbrella Sampling tutorial

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 saves

Re: [gmx-users] Umbrella Sampling tutorial

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 2

[gmx-users] Umbrella Sampling tutorial

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

Re: [gmx-users] Umbrella Sampling tutorial

On 12/1/13 9:39 AM, shahab shariati wrote: Dear Justin Thanks for your reply If I place drug molecule within the water, can I use the same Pull code parameters in the case drug molecule within lipid bilayer? pull= umbrella pull_geometry = position ; simple distance increase p

[gmx-users] Umbrella Sampling tutorial

Dear Justin Thanks for your reply If I place drug molecule within the water, can I use the same Pull code parameters in the case drug molecule within lipid bilayer? pull= umbrella pull_geometry = position ; simple distance increase pull_dim= N N Y pull_start = yes

Re: [gmx-users] Umbrella Sampling tutorial

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 bil

[gmx-users] Umbrella Sampling tutorial

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 specifi

Re: [gmx-users] Umbrella Sampling tutorial

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 pull_geometr

[gmx-users] Umbrella Sampling tutorial

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 minimizatio