Re: [gmx-users] umbrella sampling

On Mon, Nov 27, 2017 at 1:55 AM, Alex wrote: > Hi, > > The answer is clearly in the error, just read it please: > 2.848793 > 0.49 * (4/2) where 4 is the box length. > > You can either keep the “pull_coord1_geometry= distance” and increase > the box length or change

Re: [gmx-users] umbrella sampling

Hi, The answer is clearly in the error, just read it please: 2.848793 > 0.49 * (4/2) where 4 is the box length. You can either keep the “pull_coord1_geometry= distance” and increase the box length or change the “pull_coord1_geometry” to “= direction-periodic“. I prefer the former though.

[gmx-users] umbrella sampling

Hi; This is md_pull.mdp integrator = md dt = 0.001 nsteps = 200 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy= 1000 nstxtcout

Re: [gmx-users] Umbrella Sampling

On 11/26/17 1:08 PM, Roja wrote: Would you please tell me what is the difference between using umbrella in 4.5.x version and 5.1.4 version?are they different in ACCURACY of sampling? Probably. There have been thousands of bug fixes and features added since 4.5.4, which was released 6 years

Re: [gmx-users] Umbrella Sampling

Would you please tell me what is the difference between using umbrella in 4.5.x version and 5.1.4 version?are they different in ACCURACY of sampling? Sent from my iPhone > On Nov 26, 2017, at 21:14, Justin Lemkul wrote: > > > >> On 11/26/17 12:40 PM, rose rahmani wrote: >>

Re: [gmx-users] Umbrella Sampling

On 11/26/17 12:40 PM, rose rahmani wrote: Hello; what re pull_ncoords , pull_coord1_type , pull_coord1_groups (in V5.1.4) called in version 4.5.4? Why use deprecated software? We don't officially support the 4.5.x series any more. Use the newest version. Some things don't have exact

[gmx-users] Umbrella Sampling

Hello; what re pull_ncoords , pull_coord1_type , pull_coord1_groups (in V5.1.4) called in version 4.5.4? Thank you so much Rose -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Umbrella sampling

On 11/25/17 3:59 PM, rose rahmani wrote: On Sat, Nov 25, 2017 at 11:46 PM, Justin Lemkul wrote: On 11/25/17 3:07 PM, rose rahmani wrote: Oh sorry this is .mdp file: DEFINE = -DPOSRES What are you restraining? This seems counterproductive, and by

Re: [gmx-users] Umbrella sampling

On Sat, Nov 25, 2017 at 11:46 PM, Justin Lemkul wrote: > > > On 11/25/17 3:07 PM, rose rahmani wrote: > >> Oh sorry this is .mdp file: >> >> DEFINE = -DPOSRES >> > > What are you restraining? This seems counterproductive, and by default >> (unless you've hacked

Re: [gmx-users] Umbrella sampling

On 11/25/17 3:07 PM, rose rahmani wrote: Oh sorry this is .mdp file: DEFINE = -DPOSRES What are you restraining? This seems counterproductive, and by default (unless you've hacked the topology), this is going to restrain your protein, which is definitely wrong.

Re: [gmx-users] umbrella sampling

Oh sorry this is .mdp file: DEFINE = -DPOSRES integrator = md dt = 0.001 nsteps = 200 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy

Re: [gmx-users] Umbrella sampling

Oh sorry this is .mdp file: DEFINE = -DPOSRES integrator = md dt = 0.001 nsteps = 200 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy

Re: [gmx-users] umbrella sampling

On 11/25/17 12:57 PM, rose rahmani wrote: On Sat, Nov 25, 2017 at 7:01 PM, Justin Lemkul wrote: On 11/25/17 5:05 AM, rose rahmani wrote: Hi, i'm using umbrella sampling and i'm a beginner in GROMACS. as an example i got 5 dist.xvg files and then: command: perl

Re: [gmx-users] Umbrella sampling

On 11/25/17 11:49 AM, rose rahmani wrote: On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul wrote: On 11/24/17 3:32 PM, rose rahmani wrote: I attached md_pull.mdp file i put " cutoff-scheme = group" beecause of some errors (about energy groups) The use of energygrps has

Re: [gmx-users] umbrella sampling

On Sat, Nov 25, 2017 at 7:01 PM, Justin Lemkul wrote: > > > On 11/25/17 5:05 AM, rose rahmani wrote: > >> Hi, >> >> i'm using umbrella sampling and i'm a beginner in GROMACS. >> >> as an example i got 5 dist.xvg files and then: >> >> command: perl distances.pl >>> this is

Re: [gmx-users] Umbrella sampling

On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul wrote: > > > On 11/24/17 3:32 PM, rose rahmani wrote: > >> I attached md_pull.mdp file >> >> i put " cutoff-scheme = group" beecause of some errors (about energy >> groups) >> > > The use of energygrps has no effect on the physics.

Re: [gmx-users] umbrella sampling

On 11/25/17 5:05 AM, rose rahmani wrote: Hi, i'm using umbrella sampling and i'm a beginner in GROMACS. as an example i got 5 dist.xvg files and then: command: perl distances.pl this is distances.pl: #!/usr/bin/perl -w use strict; # write output to single file

Re: [gmx-users] Umbrella sampling

On 11/24/17 3:32 PM, rose rahmani wrote: I attached md_pull.mdp file i put " cutoff-scheme = group" beecause of some errors (about energy groups) The use of energygrps has no effect on the physics. You should view pairwise interactions energies as an analysis method, not something that

[gmx-users] umbrella sampling

Hi, i'm using umbrella sampling and i'm a beginner in GROMACS. as an example i got 5 dist.xvg files and then: >>command: perl distances.pl this is distances.pl: #!/usr/bin/perl -w use strict; # write output to single file open(OUT, ">>summary_distances.dat");

Re: [gmx-users] Umbrella sampling

I attached md_pull.mdp file i put " cutoff-scheme = group" beecause of some errors (about energy groups) This is what i try to do(part of some literatures); 1-pulling the CM of the object along the z-axis—perpendicular to the surface of ZnO 2-Pulling is implemented through a “dummy particle”

Re: [gmx-users] Umbrella sampling

On 11/24/17 9:14 AM, Rose wrote: Hello I'm beginner in GROMACS. I'm using umbrella sampling(helping from its tutorial with MR Lemkul) But I don't know how should I implement deltaZ and how choose different conf.gro and which will be useful for further sampling. To tell the truth I couldn't

[gmx-users] Umbrella sampling

Hello I'm beginner in GROMACS. I'm using umbrella sampling(helping from its tutorial with MR Lemkul) But I don't know how should I implement deltaZ and how choose different conf.gro and which will be useful for further sampling. To tell the truth I couldn't get summary.dat by "perl distance.pl"

[gmx-users] Umbrella Sampling

Hello; i'm using umbrella sampling and i have some basic questions about it, i will appreciate you if you help me; 1. for example i've got 2000 conf.gro and i want to choose 38 of them. i dont know how choose them eficiently???(The conformations are scanned every 0.1 ps in order to save them

[gmx-users] Umbrella Sampling

Hello; i'm using umbrella sampling and i have some basic questions about it, i will appreciate you if you help me; 1. for example i've got 2000 conf.gro and i want to choose 38 of them. i dont know how choose them eficiently???(The conformations are scanned every 0.1 ps in order to save them

[gmx-users] Umbrella Sampling

Hello i'm trying to do umbrella sampling and this is md_umbrella.mdp; DEFINE = -DPOSRES integrator = md dt = 0.001 nsteps = 4000 nstxout = 0 nstvout = 0 nstfout = 0

[gmx-users] Umbrella Sampling

Hello i'm trying to do umbrella sampling and this is part of md_umbrella.mdp; DEFINE = -DPOSRES integrator = md dt = 0.001 nsteps = 4000 nstxout = 0 nstvout = 0 nstfout

[gmx-users] Umbrella Sampling Replica Exchange

Dear all, I was surprised that my Google search for Replica Exchange for Umbrella sampling using Gromacs did not yield a positive result. Is it really not possible to perform HRE for US within the framework of Gromacs? Thanks in advance for any answer, hint, or tutorial! All the best

Re: [gmx-users] Umbrella sampling: issue with COM distance far from initial value

On Tue, Oct 17, 2017 at 8:05 AM, Giuseppe Léonardo Licari < giuseppe.lic...@unige.ch> wrote: > Dear all, > > I have troubles with umbrella sampling. During the umbrella sampling > simulation the COM distance between the two solutes is going too far from > the set initial value. I tried to

[gmx-users] Umbrella sampling: issue with COM distance far from initial value

Dear all, I have troubles with umbrella sampling. During the umbrella sampling simulation the COM distance between the two solutes is going too far from the set initial value. I tried to increase a lot the force constant of the harmonic potential. I also tried to change "umbrella" to

[gmx-users] umbrella sampling

??Hi gmx-users, I am running umbrella sampling according to the gromacs tutorial written by Justin A. Lemkul. In my system, there are two molecules (Chain_A and Chain_B) immobilized on the CNT surface with pi-stacking. I would like to calculate PMF of these two molecules (on the CNT surface)

[gmx-users] umbrella sampling

Dear gromacs developers, I am trying to implement umbrella sampling in my work but instead of distance pulling i want to do rotational pull with the gap of 10 degree. I went through your tutorial and many articles but im unable to find how to implement rotational pull in .mdp file. will you

Re: [gmx-users] umbrella sampling

On 9/2/17 10:28 AM, sp...@iacs.res.in wrote:  Hi all I am trying to do umbrella sampling of protein unfolding with radius of gyration as reaction coordinate using gromacs-2016.3 patched with plumed-2.3.2. I want to calculate free energy for the system. I am using the following command gmx

[gmx-users] umbrella sampling

Hi all I am trying to do umbrella sampling of protein unfolding with radius of gyration as reaction coordinate using gromacs-2016.3 patched with plumed-2.3.2. I want to calculate free energy for the system. I am using the following command gmx wham P=1.4 1.5 100 0.001 300 0 metadata.dat  

[gmx-users] umbrella sampling

Hi all I am trying to do umbrella sampling of protein with radius of gyration as reaction coordinate using gromacs-2016.3 patched with plumed-2.3.2. I have chosen 13 configurations of protein for sampling. Now I want to analyse the data. So how to plot histogram and PMF w.r.t radius of gyartion?

[gmx-users] Umbrella Sampling -PME

Hello, will decouple intramuscular interactions during windows simulation impact the accuracy of the PME estimated? I am pulling large molecule Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] Umbrella Sampling with Direction-Periodic

Hello, I am using a pull code with geometry=direction-periodic and attempting to use gmx wham to construct the free energy. The pulling code is doing what I would like it to, but as might be expected from direction-periodic, when the pull distance is more than half the box length the distance is

[gmx-users] Umbrella Sampling with Direction-Periodic Pulling

Hello, I am using a pull code with geometry=direction-periodic and attempting to use gmx wham to construct the free energy. I believe the pulling code is doing what I would like it to, but as might be expected from direction-periodic, when the pull distance is more than half the box length the

Re: [gmx-users] umbrella sampling

On 7/11/17 5:29 PM, Ben Tam wrote: Hi Justin, Thanks for answering. I have tried sending the histogram however it is too big of a file. But the histogram shows a lot of overlapping and multiple peaks. All of the value in profile.xvg showing nan. What can that mean?

Re: [gmx-users] umbrella sampling

edu> Sent: Tuesday, July 11, 2017 18:07 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] umbrella sampling On 7/11/17 12:53 PM, Ben Tam wrote: Hi Andre, Thanks for your answer. Actually I should clarify it is metal-organic-framework that I am working on which is a porous material. With

Re: [gmx-users] umbrella sampling

behalf of Justin Lemkul <jalem...@vt.edu> Sent: Tuesday, July 11, 2017 18:07 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] umbrella sampling On 7/11/17 12:53 PM, Ben Tam wrote: > Hi Andre, > > > Thanks for your answer. Actually I should clarify it is > metal-organic-framework

Re: [gmx-users] umbrella sampling

users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of André Farias de Moura <mo...@ufscar.br> Sent: Tuesday, July 11, 2017 17:44 To: Discussion list for GROMACS users Subject: Re: [gmx-users] umbrella sampling I never did it myself, but gene

Re: [gmx-users] umbrella sampling

of André Farias de Moura <mo...@ufscar.br> Sent: Tuesday, July 11, 2017 17:44 To: Discussion list for GROMACS users Subject: Re: [gmx-users] umbrella sampling I never did it myself, but generally speaking you don' t expect that there' s a lot of room inside a crystal for any molecule to dif

Re: [gmx-users] umbrella sampling

I never did it myself, but generally speaking you don' t expect that there' s a lot of room inside a crystal for any molecule to diffuse there, especially when it comes to cross something like a crystallographic plane, meaning that huge energy barriers should be there, leading to NaN and other

[gmx-users] umbrella sampling

Dear All, I am doing umbrella sampling for a water molecules moving inside a crystal structure, however I am running into a problem on the output file with profile.xvg all value showing “nan”. This error has occurred when I reduce the slide width from 0.2 nm to 0.1 nm. I have used the exact

Re: [gmx-users] Umbrella sampling

On 6/14/17 10:52 PM, Kingsley Theras Primus Dass . wrote: Hii I am trying out the umbrella sampling tutorial. I finished generating a series of coordinate file , but when i run the perl script the summary_distance.dat doesnt generate the COM distance value What would be the possible

[gmx-users] Umbrella sampling

Hii I am trying out the umbrella sampling tutorial. I finished generating a series of coordinate file , but when i run the perl script the summary_distance.dat doesnt generate the COM distance value What would be the possible reason for this ? Thank you Kingsley -- Gromacs Users mailing

Re: [gmx-users] Umbrella sampling and PMF calculations

> > >> > A pull vector can indeed not be (0, 0, 0) but that's not a pull rate. The pull vector is exactly as set by you to N N Y, maybe the code multiplies the vector components by the corresponding pull rates and then checks the resulting velocity vector, I don't know, but the error is there

Re: [gmx-users] Umbrella sampling and PMF calculations

On 6/2/17 6:40 PM, Alex wrote: I find that surprising. Please provide the full, exact error and your pull settings. All of the geometries should work with zero or non-zero pull rates. But I admit, it has been many years since I used GROMACS with the pull code. Simply take your pull

Re: [gmx-users] Umbrella sampling and PMF calculations

> > I find that surprising. Please provide the full, exact error and your >> pull settings. All of the geometries should work with zero or non-zero >> pull rates. But I admit, it has been many years since I used GROMACS with >> the pull code. >> > Simply take your pull code from the tutorial and

Re: [gmx-users] Umbrella sampling and PMF calculations

On 6/2/17 4:17 PM, Alex wrote: So, Justin, just to follow up here. With 'cylinder', grompp refuses to accept a zero pulling rate. This begs a different question: in my I find that surprising. Please provide the full, exact error and your pull settings. All of the geometries should work

Re: [gmx-users] Umbrella sampling and PMF calculations

So, Justin, just to follow up here. With 'cylinder', grompp refuses to accept a zero pulling rate. This begs a different question: in my particular system, the COM position coincides with the center of the single reactive pore at the geometric center of the membrane. Why even bother with this

Re: [gmx-users] Umbrella sampling and PMF calculations

Yes, because if your ion diffuses laterally (or whatever constitutes your "hole"), then you're not sampling what you think you're sampling. That's what the cylinder geometry is for. You have a system capable of significant lateral movement, so if you fail to apply a bias that acts in

Re: [gmx-users] Umbrella sampling and PMF calculations

On 6/1/17 6:35 PM, Alex wrote: You have a membrane with water on either side, yes? That's a layered system. But frankly, at this point I don't follow at all what you're trying to do. - Let me try from the beginning. :) A membrane in XY, water on both sides. At the center of the

Re: [gmx-users] Umbrella sampling and PMF calculations

> > >> > You have a membrane with water on either side, yes? That's a layered > system. > > But frankly, at this point I don't follow at all what you're trying to do. > > - Let me try from the beginning. :) A membrane in XY, water on both sides. At the center of the membrane, there is a

Re: [gmx-users] Umbrella sampling and PMF calculations

On 6/1/17 6:16 PM, Alex wrote: Your situation is completely different. Look into the cylinder settings for dealing with a layered system, but I have no experience with them. To be clear - you always need two groups to define the vector (reaction coordinate) along which the bias is

Re: [gmx-users] Umbrella sampling and PMF calculations

> > >> > Your situation is completely different. Look into the cylinder settings > for dealing with a layered system, but I have no experience with them. To > be clear - you always need two groups to define the vector (reaction > coordinate) along which the bias is applied. So you need to

Re: [gmx-users] Umbrella sampling and PMF calculations

On 6/1/17 4:28 PM, Alex wrote: Just a few quick questions for Justin. I am looking at your tutorial, starting here: http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html 1. In your example, you have two pull groups. My understanding is that both are pulled

[gmx-users] Umbrella sampling and PMF calculations

Just a few quick questions for Justin. I am looking at your tutorial, starting here: http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html 1. In your example, you have two pull groups. My understanding is that both are pulled relative to each other. In my case,

[gmx-users] UMBRELLA SAMPLING

Hi gromacs users, I want to perfom NVT equilibration, pull code (using pull-geometry = direction-periodic) Prior to this step, energy minimization (500 steps) and NPT equilibration (5 steps) was done As I am new to gromacs and simulations, can anyone tell me whether the following NVT

Re: [gmx-users] UMBRELLA SAMPLING

On 3/4/17 9:24 AM, Subashini .K wrote: Hi gromacs users, I want to calculate delta G for protein ligand binding. Had run the umbrella pulling simulation for 100 ps (protein ligand solvated in water), applying restraint in the protein (using the code in gromacs tutorial website,

[gmx-users] UMBRELLA SAMPLING

Hi gromacs users, I want to calculate delta G for protein ligand binding. Had run the umbrella pulling simulation for 100 ps (protein ligand solvated in water), applying restraint in the protein (using the code in gromacs tutorial website, Bevenlab). But, after running the perl script

[gmx-users] UMBRELLA SAMPLING

Hi gromacs users, I want to calculate the binding energy (ΔGbind) using umbrella sampling method (between protein and ligand which is solvated in water) How to custom index groups for the pulling simulation? The protein under consideration has only one chain A. Thanks, Subashini.K --

[gmx-users] umbrella sampling pulling direction

Dear all, My ligand is somewhat inside the protein and im confused in which direction i should pull the ligand for umbrella sampling. I have attached the *.gro file. In my previous US systems ligand was on the 'surface of the protein' so that it was easy to pull on y or z- direction.

Re: [gmx-users] umbrella sampling distances

On 11/17/16 10:06 PM, Irem Altan wrote: Hi, I’m trying to apply umbrella sampling to a system following Justin Lemkul’s tutorial. I’m confused about how the distances are calculated, however. When I run a pull simulation and calculate center of mass distances with gmx distance, I see that

[gmx-users] umbrella sampling distances

Hi, I’m trying to apply umbrella sampling to a system following Justin Lemkul’s tutorial. I’m confused about how the distances are calculated, however. When I run a pull simulation and calculate center of mass distances with gmx distance, I see that the distance in the 0th configuration is

Re: [gmx-users] Umbrella Sampling

Hey, Did you change the number inside the distances.pl script? If you have 1000 files, you need to change the number of 500 on line 6, 13 , and 36 (lines start with for loop) make them 1000. > On 13 Nov 2016, at 11:10, Mouri Ahmed wrote: > > Hi everyone, > > I have

[gmx-users] Umbrella Sampling

Hi everyone, I have run pulling simulation for the protein complex system. I have got 1000 configuration files. And in the summary_distances.dat, I have found 0-500 distances. How will I select configuration file for the npt_umbrella simulation. Thanks in advance. I will be very grateful for

[gmx-users] Umbrella Sampling - LINCS error when pull group is in vapor phase

Hi, I am trying to calculate the adsorption free energy of a molecule onto water. I want to use umbrella sampling to obtain the free energy profile as a function of distance normal to a water surface. I am getting LINCS error when my molecule is in the vapor phase. The error messages indicate

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

[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

On 11/6/16 1:53 AM, m g wrote: Dear Justin, In umbrella sampling tutorial, what force constant was used during the umbrella sampling simulations? Please read the contents of the .mdp files provided in the tutorial. -Justin -- == Justin A.

[gmx-users] Umbrella sampling

Dear Justin, In umbrella sampling tutorial, what force constant was used during the umbrella sampling simulations? Many thanks, Mr. Ganj -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

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

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

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

[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

Re: [gmx-users] Umbrella sampling

On 9/5/16 3:16 AM, masoud aliyar wrote: Hi everybody I’m trying to do Umbrella Sampling by using Justin’s tutorial. Everything is ok but some aspects of the procedure remain a bit unclear to me. Why don’t we need to do NVT equilibration before first MD? And why pull codes Equilibrate however

[gmx-users] Umbrella sampling

Hi everybody I’m trying to do Umbrella Sampling by using Justin’s tutorial. Everything is ok but some aspects of the procedure remain a bit unclear to me. Why don’t we need to do NVT equilibration before first MD? And why pull codes are applied during NPT equilibration of selected windows or

Re: [gmx-users] umbrella sampling pull to -z direction

On 8/19/16 9:32 AM, Nikhil Maroli wrote: Dear Justin, Thanks for your answer, I tried with pull_coord1_rate = -0.01 but its not working ,the ligand is going 'inside' the protein I have tried with pull_coord1_geometry= direction *pull-coord1-vec = 0 0 -1* *still same results*

Re: [gmx-users] umbrella sampling pull to -z direction

Dear Justin, Thanks for your answer, I tried with pull_coord1_rate = -0.01 but its not working ,the ligand is going 'inside' the protein I have tried with pull_coord1_geometry= direction *pull-coord1-vec = 0 0 -1* *still same results* *Could you tell me where im wrong?* -- Gromacs

Re: [gmx-users] umbrella sampling pull to -z direction

On 8/19/16 7:59 AM, Nikhil Maroli wrote: Dear all, I wanted to do an US of a protein-ligand system, my ligand is situated on -z direction as in Fig (below link) if I change the option pull_coord1_dim = N N Y to pull_coord1_dim = N N -Y it will work or is ther any way to

[gmx-users] umbrella sampling pull to -z direction

Dear all, I wanted to do an US of a protein-ligand system, my ligand is situated on -z direction as in Fig (below link) if I change the option pull_coord1_dim = N N Y to pull_coord1_dim = N N -Y it will work or is ther any way to deal in this situations?

Re: [gmx-users] umbrella sampling for determining interfacial energy

Thank you very much.​ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

Re: [gmx-users] umbrella sampling for determining interfacial energy

Hi, this is a good coincidence, but I think I do something very similar to what you just described. I use umbrella sampling to estimate the free energy profile as a function of distance from a liquid-vapor interface. Then, the free energy cost of adsorption to the interface can be approximated. I

Re: [gmx-users] Umbrella Sampling (Justin Lemkul)

Hi already it is answered. run the gmx distance command to understand the problem. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For

Re: [gmx-users] Umbrella Sampling (Justin Lemkul)

Hello all, I was practicing the umbrella sampling tutorial by Dr. Justin Lemkul. In my summary_distances.dat file there is only one column ( the column for centre of mass is missing ). Can anyone say what possible mistakes I must have done. Regards, Amit Behera Dept. of Chemical Engg., IISc,

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.

[gmx-users] Umbrella Sampling - choice of pull-coord?-dim

Dear GROMACS users, I am interested in the role of the mdp parameter pull-coord?-dim when sampling a particular umbrella window after having generated initial configurations for, say, the COM distance between two groups being the reaction coordinate. I know that these options can be controlled

Re: [gmx-users] Umbrella sampling version 5.0

On 5/3/16 9:18 PM, Steve Seibold wrote: I have used the older version of Gromacs 4.x.x to do umbrella sampling; I have just installed Gromacs 5.0 and found that the tutorials on line are now for Gromacs 5.1. Is there a huge difference in the protocol from 5.0 to 5.1? I used a youtube

[gmx-users] Umbrella sampling version 5.0

I have used the older version of Gromacs 4.x.x to do umbrella sampling; I have just installed Gromacs 5.0 and found that the tutorials on line are now for Gromacs 5.1. Is there a huge difference in the protocol from 5.0 to 5.1? I used a youtube illustration to install Gromacs. I tried to

[gmx-users] Umbrella sampling without pull

Himy question is , can we use Umbrella Sampling without Pulling, Is it possible? i know the concept of Umbrella sampling and Replica Exchange, i have performed solvation of different small molecules in water and calculated energies. some of results are not good, so how can i improve these

Re: [gmx-users] Umbrella sampling along PCA eigenvector using make_edi

Dear Hendrik, that indeed looks a bit strange. If you provide the necessary input files for a test, I could have a look at what might be wrong. You can put them somewhere for download or email them directly to me (not to the list, they will not be accepted). Carsten > On 30 Mar 2016, at 16:11,

[gmx-users] Umbrella sampling along PCA eigenvector using make_edi

Hi everyone, I want to do umbrella sampling along a PCA eigenvector using 'gmx make_edi'. The eigenvectors of the protein backbone atoms were computed using 'gmx covar'. The command for generating the 'sam.edi' file looks like the following: gmx make_edi -s topol.tpr -f eigenvec.trr -eig

Re: [gmx-users] Umbrella sampling error with drug molecule

On 3/1/16 7:59 PM, Khuong Truong Gia wrote: Hi all, I am using gromacs to run umbrella sampling simulation with a drug molecule (polymer). I got force field from PRODRG. When run pulling the drug I got this error: step 86530014: Water molecule starting at atom 8336 can not be settled. Check

[gmx-users] Umbrella sampling error with drug molecule

Hi all, I am using gromacs to run umbrella sampling simulation with a drug molecule (polymer). I got force field from PRODRG. When run pulling the drug I got this error: step 86530014: Water molecule starting at atom 8336 can not be settled. Check for bad contacts and/or reduce the timestep if

[gmx-users] Umbrella Sampling, Analysis Step

Dear Gromacs users, I've run the umbrella sampling. I could draw histograms with sufficient overlap, so I determined all of the simulations reached enough length of time. Now it's the analysis step. When I chose tpr files and pullf.xvg (forces) files as the input to wham, I was able to

[gmx-users] umbrella sampling error

Dear all, im running umbrella sampling when invoke the following command i got the follwoing warnings and grompp terminated becasue of so much warning ,initially i neutralised the My protein-Ligand system with NACl,so how come there will be a charge? (NOTE 5)what i can do for that? can i use

Re: [gmx-users] umbrella sampling error

On 1/5/16 5:36 AM, Nikhil Maroli wrote: Dear all, im running umbrella sampling when invoke the following command i got the follwoing warnings and grompp terminated becasue of so much warning ,initially i neutralised the My protein-Ligand system with NACl,so how come there will be a charge?

[gmx-users] Umbrella Sampling and GPU

Dear users, i would like to perform Umbrella sampling on few protein-ligand system, i wanted to know is it possible to run it in GPU? (Tesla k20) Thanks -- Ragards, Nikhil Maroli -- Gromacs Users mailing list * Please search the archive at

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