[gmx-users] PMF in inhomogeneous fluid phase

Dear Gromacs-users, I have a question that may not be directly Gromacs-related. I want to calculate the potential of mean force (PMF) for a solute that is pulled away from a crystal surface. The issue is that the fluid phase is inhomogeneous, as it consists of water and cluster-forming ions.

[gmx-users] PMF wrong when calculating dihedral angle rotate

Dear gmx users, I want to repeat a amber tutorial *http://ambermd.org/tutorials/advanced/tutorial17/index.htm * by using gromacs, which is about PMF calculation of Alanine Dipeptide Phi/Psi Rotation. Everything is ok about the process

[gmx-users] PMF from constant force..

Dear all, Is there any way to obtain PMF from; pull = constant force.? I have seen wham only supports 'umbrella' When i try to use umbrella my molecule is not travelling through the channel. Thanks in advance. -- Regards, Nikhil Maroli -- Gromacs Users mailing list * Please search the

[gmx-users] PMF calculation: molecule though the channel.

Dear all, Im trying to pull water molecules through Aquaporin channel with the following pull parameters (to obtain PMF). On visualising the trajectory, water molecules travelling around the surface/outside of aquaporin instead of going through inside. How I can make sure that the water molecule

[gmx-users] PMF ligand membrane protein

Dear Gromacs User, this is the first time I am attempting membrane protein simulation. I wish to obtain a PMF value for a ligand permeating through a membrane protein (lacY permease). In the Xray str. the ligand is almost at the center of the protein. I wish to generate enough initial

Re: [gmx-users] PMF - US histograms problem

Hi, When I get a region sparsely populated like that, I increase the number of points in that particular region and increase the k value to about 3000 but not more than that. Increasing the k value to something like 2 will result in the distribution getting very narrow and therefore further

[gmx-users] PMF - US histograms problem

Hi everyone, I'm trying to calculate the PMF for the extraction of a peptide from within a peptide nanostructure. However I'm having difficulty to overlap the histograms for the first pulling windows: Many full overlap windows follow by a large gap with no histogram. I've tried the two things I

Re: [gmx-users] PMF, Enthalpy, Entropy

On 14/03/17 13:23, Justin Lemkul wrote: On 3/13/17 2:11 PM, Alex wrote: Hello all, I have the calculated the PMF for the adsorption of a peptide into a solid surface using umbrella sampling, a 60 ns of NVT-production for each window was considered so that the PMF is well converged. Now,

Re: [gmx-users] PMF, Enthalpy, Entropy

On 3/13/17 2:11 PM, Alex wrote: Hello all, I have the calculated the PMF for the adsorption of a peptide into a solid surface using umbrella sampling, a 60 ns of NVT-production for each window was considered so that the PMF is well converged. Now, following a nice paper by Prof. van der Spoel

[gmx-users] PMF, Enthalpy, Entropy

Hello all, I have the calculated the PMF for the adsorption of a peptide into a solid surface using umbrella sampling, a 60 ns of NVT-production for each window was considered so that the PMF is well converged. Now, following a nice paper by Prof. van der Spoel "*DOI: *10.1021/ct400404q" and in

[gmx-users] PMF simulation in Gromacs 2016.1

Dear Gromacs users, I am comparing the PMF simulations using the Gromacs 2016 version with old version 5.0.5. I found the *gmx wham* in Gromacs 5.0.5 couldn't process the tpr files generated by Gromacs 2016.1 . (tpx version 100 vs. tpx version 110). The new Gromacs 2016.1 can process the tpr

Re: [gmx-users] PMF changing drastically with the number of bins

Dear all, I have made mistake. I didn't compare the value of free energy at the minimum with the plateau value. At all three bin numbers the difference is close to 2 kCal mol-1. So this is solved. Best regards Sajeewa On Mon, Dec 19, 2016 at 1:15 PM, Sajeewa Pemasinghe

[gmx-users] PMF changing drastically with the number of bins

Dear all, I am calculating the PMF as the COM distance of two molecules are changing using umbrella sampling ( pull = umbrella ). Each umbrella sampling simulation runs for 50ns. When I calculate the PMF with default (200 bins) settings using gmx wham I get the minimum in free energy of -1.19

Re: [gmx-users] PMF decompostion

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Salman Zarrini <salman.zarr...@gmail.com> Sent: 02 December 2016 17:16:15 To: gmx-us...@gromacs.org Subject: [gmx-users] PMF decompostion Dear gromacs user, I was

Re: [gmx-users] PMF decompostion

>>> thermodynamically meaningful components here. VDW and Q does not mean >>> anything outside the force field definition since they can not be >>> measured >>> in any way. For more info on decomposing into enthalpy and entropy, see >>> this paper: http://pub

Re: [gmx-users] PMF decompostion

sys.kth.se> on behalf of Salman Zarrini <salman.zarr...@gmail.com> Sent: 02 December 2016 17:16:15 To: gmx-us...@gromacs.org Subject: [gmx-users] PMF decompostion Dear gromacs user, I was wondering if something has been already implemented in gromacs to make possible the potential of mean

Re: [gmx-users] PMF decompostion

g_gmx-users-boun...@maillist.sys.kth.se < >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Salman >> Zarrini <salman.zarr...@gmail.com> >> Sent: 02 December 2016 17:16:15 >> To: gmx-us...@gromacs.org >> Subject: [gmx-users] PMF decompostion

Re: [gmx-users] PMF decompostion

02 December 2016 17:16:15 To: gmx-us...@gromacs.org Subject: [gmx-users] PMF decompostion Dear gromacs user, I was wondering if something has been already implemented in gromacs to make possible the potential of mean force (PMF) decomposition into the van der waals and electrostatic energies? Woul

Re: [gmx-users] PMF decompostion

. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Salman Zarrini <salman.zarr...@gmail.com> Sent: 02 December 2016 17:16:15 To: gmx-us...@gromacs.org Subject: [gmx-users] PMF decomp

[gmx-users] PMF decompostion

Dear gromacs user, I was wondering if something has been already implemented in gromacs to make possible the potential of mean force (PMF) decomposition into the van der waals and electrostatic energies? Would you please also let me know if the desolvation energy originated from protein-water or

Re: [gmx-users] pmf settings

On 11/17/16 5:33 AM, Qasim Pars wrote: Dear users, I am trying to calculate the binding free energy between protein and ligand using the PMF. I will add the below pull code lines to my production run mdp file. pull= umbrella pull_geometry = distance pull_dim= Y Y Y

[gmx-users] pmf settings

Dear users, I am trying to calculate the binding free energy between protein and ligand using the PMF. I will add the below pull code lines to my production run mdp file. pull= umbrella pull_geometry = distance pull_dim= Y Y Y pull_start = yes pull_ngroups= 2

Re: [gmx-users] pmf

On 10/28/16 4:20 PM, Alex wrote: Thanks for your response. The version for all tasks is "gmx, VERSION 5.1.2". I hope extra windows would be required just in the gaps, not in the whole reaction path. Yes, you just need more windows. I had 81 windows spacing mostly 0.01 nm and in the end

Re: [gmx-users] pmf

Thanks for your response. The version for all tasks is "gmx, VERSION 5.1.2". I hope extra windows would be required just in the gaps, not in the whole reaction path. I had 81 windows spacing mostly 0.01 nm and in the end 0.04 nm. The peptide surly has many rotations from top of the surface to

Re: [gmx-users] pmf

On 10/28/16 4:04 PM, Alex wrote: Dear Gromacs user, Below are the result of PMF simulation of a peptide adsorbed into a solid surface. Would you please comment on them in order to improve the result. The force constant in the umberela sampling is 1100. For each windows: 1.2 ns NVT

[gmx-users] pmf

Dear Gromacs user, Below are the result of PMF simulation of a peptide adsorbed into a solid surface. Would you please comment on them in order to improve the result. The force constant in the umberela sampling is 1100. For each windows: 1.2 ns NVT equilibration followed by 2 ns of NPT and 15

Re: [gmx-users] PMF

The negative and positive in the the reaction coordinate comes probably from interaction of peptide with surface in bottom slab and top(next cell beacuse of PBC) slab in the Z direction. But I was always taking care about sampled windows so that the peptide pulled away from top of bottom surface

Re: [gmx-users] PMF

Thanks for your response. Actually I fully followed your tutorial. the pull-coord1-rate = 0.007 indicated in the pdf file is just for the pulling step and then in the next step I have pull-coord1-rate = 0.0 for each windows. Can we do the pulling step with pull-coord1-rate = 0.0 !? Regards,

Re: [gmx-users] PMF

On 10/11/16 4:01 PM, Alex wrote: Dear gromacs user, I am trying to simulate the PMF a small peptide adsorbed to a solid surface but no success unfurtunatly. For some force constant the peptide would not desorbed from the surface and for higher force constants what you can see in enclosed file

[gmx-users] PMF

Dear gromacs user, I am trying to simulate the PMF a small peptide adsorbed to a solid surface but no success unfurtunatly. For some force constant the peptide would not desorbed from the surface and for higher force constants what you can see in enclosed file will happen. Some question is: If it

Re: [gmx-users] PMF and lack if NPT equilibration

Thanks. I used the "direction-periodic", along with "semiisotropic" with zero compressibility in Z direction to have also NPT equilibration in each windows. Below is the final pressure after NPT equilibration with 1 bar reference, I hope it would be ok?! Energy Average

Re: [gmx-users] PMF and lack if NPT equilibration

On 10/10/16 4:57 AM, Alex wrote: Thanks for your response. My question is not in the sampling step as I have already pulled away two parts and even picked out the configuration of each windows. But my question is about simulation in each individual windows toward WHAM. You means in the step

Re: [gmx-users] PMF and lack if NPT equilibration

Thanks for your response. My question is not in the sampling step as I have already pulled away two parts and even picked out the configuration of each windows. But my question is about simulation in each individual windows toward WHAM. You means in the step six of the tutorial no necessarily

Re: [gmx-users] PMF and lack if NPT equilibration

On 10/8/16 2:46 PM, Alex wrote: Dear gromacs user, In a PMF simulation of a short peptide on solid surface, I am using the "direction-periodic" as "pull-coord1-geometry" in the Z direction, then as you know the equilibration of the system in NPT ensemble is not doable for the individual

[gmx-users] PMF and lack if NPT equilibration

Dear gromacs user, In a PMF simulation of a short peptide on solid surface, I am using the "direction-periodic" as "pull-coord1-geometry" in the Z direction, then as you know the equilibration of the system in NPT ensemble is not doable for the individual windows. So, for each windows of

[gmx-users] PMF of a short peptide on a solid surface

Dear gromacs user, In order to simulate the PMF of a adsorbed short peptide on a solid surface, first I minimised and equlibrated(NVT and NPT) the system and then I did a 60 ns of production run in which the peptide fully adsorbed to the surface. I used these out put to pull away the peptide from

Re: [gmx-users] PMF steadily increasing

behalf of Lukas Zimmermann <luk.zi...@gmail.com> Sent: 20 June 2016 06:03:51 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] PMF steadily increasing Thank you again for your remarks. This is what I found so far: (1) With gmx mindist it was very clear that protein and peptide do not interact. Fo

Re: [gmx-users] PMF steadily increasing

mes unbound and can >> then sample full X and Y, but on its own that should not continue to impact >> the sampling after contact is permanently broken. >> >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >> gromacs.org_gmx-users-boun...@maillist.sy

Re: [gmx-users] PMF steadily increasing

> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Lukas > Zimmermann <luk.zi...@gmail.com> > Sent: 15 June 2016 12:45:51 > To: gmx-us...@gromacs.org > Subject

Re: [gmx-users] PMF steadily increasing

is permanently broken. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Lukas Zimmermann <luk.zi...@gmail.com> Sent: 15 June 2016 12:45:51 To: gmx-us...@gromacs.org Subject: [gmx-users]

[gmx-users] PMF steadily increasing

Dear GROMACS community, I performed umbrella sampling study to estimate the binding free energy between a globular protein with 568 residues and a small peptide with 13 residues. I use the pull code with k = 800 and rate = 0.005 to generate the initial conformations over the time course of 1200

[gmx-users] PMF of a single water molecule respect to a surface

Dear Gromacs user, I am calculation the PMF of a single water molecule to pull it away from top of metallic surface along vacuum in the Z direction ,following the Justin umbrella tutorial. I am only interested in the behavior of PMF in 0.002 nm to 0.8 nm intervalon top of the surface, but I do

Re: [gmx-users] PMF of a single water molecule respect to a surface

On 2/12/16 8:47 AM, Alexander Alexander wrote: Dear Gromacs user, I am calculation the PMF of a single water molecule to pull it away from top of metallic surface along vacuum in the Z direction ,following the Justin umbrella tutorial. I am only interested in the behavior of PMF in 0.002 nm

[gmx-users] pmf-gwham

Dear All, I am doing umbrella sample for a system and I have a question. on my system I have extra two angle_restraints_z on the pulled group, and one position restrain on the reference group. Dose g-wham accept having this number of restrains on the system. Dose having many restrains

Re: [gmx-users] PMF calculation_ Constraint

Dear Justin. Thanks for response. I used constraint method because I wanted to calculate MSD, How does using a bigger box helps me? because when I make box bigger, I need to run a little bit to equilibrate system, and again the tocopherol can move and come out of the box. On Tue, Sep 22, 2015 at

[gmx-users] PMF calculation_ Constraint

Dear Gromacs users I want to calculate the PMF of tocopherol in DMPC bilayer system. For this means, I used Constraint method. the pull code in my .mdp file is : pull = constraint pull-geometry = distance;distance, direction, or cylinder pull-dim = N N Y pull-constr-tol = 1e-6 pull-start =

Re: [gmx-users] PMF calculation_ Constraint

On 9/22/15 3:46 PM, Sepideh Kavousi wrote: Dear Gromacs users I want to calculate the PMF of tocopherol in DMPC bilayer system. For this means, I used Constraint method. the pull code in my .mdp file is : pull = constraint pull-geometry = distance;distance, direction, or cylinder

Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0

Neale chris.ne...@alum.utoronto.ca To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti) Message-ID: blupr03mb184037e6ef2ec6d63bebe21c5...@blupr03mb184.namprd03.prod.outlook.com Content-Type: text

Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0

...@alum.utoronto.ca To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti) Message-ID: blupr03mb184037e6ef2ec6d63bebe21c5...@blupr03mb184.namprd03.prod.outlook.com Content-Type: text/plain

Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0

/ -- Message: 2 Date: Sun, 26 Jul 2015 02:45:50 + From: Christopher Neale chris.ne...@alum.utoronto.ca To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti) Message-ID

Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0

/ -- Message: 2 Date: Sun, 26 Jul 2015 02:45:50 + From: Christopher Neale chris.ne...@alum.utoronto.ca To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti) Message-ID

Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti)

...@gmail.com Sent: 24 July 2015 16:47 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti) Hello Chris, I write to report the results of the tests you suggested. To recap, I have two problems to solve. 1) The bad sampling

Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti)

...@gromacs.org Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 Message-ID: blupr03mb18470a33a4e3ff149c95963c5...@blupr03mb184.namprd03.prod.outlook.com Content-Type: text/plain; charset=iso-8859-1 Dear Eudes: There are two issues: The first issue is the fact

Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0

gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Eudes Fileti fil...@gmail.com Sent: 18 July 2015 21:06 To: gmx-us...@gromacs.org Subject: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 Hello guys, I'm trying to calculate the PMF using umbrella sampling for a small molecule

[gmx-users] PMF using umbrella sampling and Gromacs 5.0

Hello guys, I'm trying to calculate the PMF using umbrella sampling for a small molecule to penetrate a lipid membrane. The 1D reaction coordinate is along the z axis, which corresponds to the bilayer normal. The umbrella potential acts on the center of mass of the molecule. The initial

Re: [gmx-users] PMF calculation with constraint distance

On 5/21/15 5:19 PM, leila salimi wrote: Thanks Justin. Yes I have done PMF with Blue moon ensemble with DFT. Now I want to do the same with gromacs to have some knowledge about my FF parameters and compare with my DFT results! You meant I have to do with different configuration and average

[gmx-users] PMF calculation with constraint distance

Hi all, I started to calculate PMF between two ions in solution and I used constraint for pull option, instead of umbrella as I saw in Umbrella sampling Tutorial of Justin. This is the part of my mdp file! ; Pull code pull= constraint; Justin's value was umbrella pull_geometry

Re: [gmx-users] PMF calculation with constraint distance

On 5/21/15 5:00 PM, leila salimi wrote: Hi all, I started to calculate PMF between two ions in solution and I used constraint for pull option, instead of umbrella as I saw in Umbrella sampling Tutorial of Justin. This is the part of my mdp file! ; Pull code pull= constraint;

Re: [gmx-users] PMF calculation with constraint distance

Thanks Justin. Yes I have done PMF with Blue moon ensemble with DFT. Now I want to do the same with gromacs to have some knowledge about my FF parameters and compare with my DFT results! You meant I have to do with different configuration and average the forces? I am wondering that I did in DFT

Re: [gmx-users] PMF calculation by umbrella sampling simulations

On 4/30/15 4:12 PM, MPI wrote: Hi Justin, Thanks for your explanation. (1) In the tutorial, then what is a good approximate value of free energy ? if one follows the protocol. Is -37 or so kcal mol^-1 ? That is what you should get from the tutorial. Here, 26 windows of COM

Re: [gmx-users] PMF calculation by umbrella sampling simulations

Hi Justin, Thanks for your explanation. (1) In the tutorial, then what is a good approximate value of free energy ? if one follows the protocol. Is -37 or so kcal mol^-1 ? Here, 26 windows of COM distances are used, each for 10 ns simulation. (2) In your original paper, -50.5 kcal

[gmx-users] PMF calculation by umbrella sampling simulations

Dear Users, With GMX 4.6.5, I tried to reproduce a system of the dissociation of a single peptide in an AB42 protofibril with PMF (potential of mean force) calculation in Justin's umbrella sampling tutorial. He derived the binding energy from PMF from a series of umbrella sampling simulations

Re: [gmx-users] PMF and RDF

On 12/9/14 11:51 PM, sujithkakkat . wrote: Hi Erik and Justin, Thanks for the response. Erik, I was thinking that in the case of hydrophobic solutes, there is a higher chance of proper sampling of all points along the inter solute distance. I believe the water shell around the

Re: [gmx-users] PMF and RDF

Dear Sujith, Umbrella sampling does exactly that, but adds a biasing potential to sample high-energy regions of the reaction coordinate in separate simulations. The -px output when you do umbrella sampling with mdrun is indeed a sampling of distances along the reaction coordinate, which if you

Re: [gmx-users] PMF and RDF

On 12/9/14 1:39 AM, sujithkakkat . wrote: Dear all, I read in *Phys. Chem. Chem. Phys., 2009, 11, 10427-10437*, that the radial distribution function is directly related to Potential of mean force through RDF=exp(-PMF/kT). My question is why would someone worry about computing

Re: [gmx-users] PMF and RDF

On 9 Dec 2014, at 11:00, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Dear Sujith, Umbrella sampling does exactly that, but adds a biasing potential to sample high-energy regions of the reaction coordinate in separate simulations. The -px output when you do umbrella sampling with

Re: [gmx-users] PMF and RDF

Hi Erik and Justin, Thanks for the response. Erik, I was thinking that in the case of hydrophobic solutes, there is a higher chance of proper sampling of all points along the inter solute distance. I believe the water shell around the hydrophibic solvent can break easier than the that in the

[gmx-users] PMF and RDF

Dear all, I read in *Phys. Chem. Chem. Phys., 2009, 11, 10427-10437*, that the radial distribution function is directly related to Potential of mean force through RDF=exp(-PMF/kT). My question is why would someone worry about computing PMF in a simple case like interaction between two

Re: [gmx-users] PMF curve in umbrella sampling

On 8/30/14, 8:09 AM, Mana Ib wrote: Thankyou for your response. I spaced them at approx 0.05nm because at the 473rd configuration my ligand becomes solvated...and completely dissociated from the protein and there is a jump in the COM distances. Would you recommend running windows for

Re: [gmx-users] PMF curve in umbrella sampling

Thankyou for your response. I spaced them at approx 0.05nm because at the 473rd configuration my ligand becomes solvated...and completely dissociated from the protein and there is a jump in the COM distances. Would you recommend running windows for configurations beyond 473 to get an accurate PMF

[gmx-users] PMF curve in umbrella sampling

Dear Users, I am doing an umbrella sampling for a protein-ligand complex, wherein I first did an SMD run for 500 ps and generated 500 configurations, the COM distances for these configurations start at 1.25nm for conf0 and so on till 6.4nm for conf500. Hence I used a 0.05nm spacing to select

Re: [gmx-users] PMF curve in umbrella sampling

On 8/29/14, 2:08 PM, Mana Ib wrote: Dear Users, I am doing an umbrella sampling for a protein-ligand complex, wherein I first did an SMD run for 500 ps and generated 500 configurations, the COM distances for these configurations start at 1.25nm for conf0 and so on till 6.4nm for conf500.

[gmx-users] PMF calculation with three reaction coordinates

Dear gromacs users, I am running an umbrella pulling to calculate the PMF of a soft protein adsorbed on surface. Since the protein is soft (easy to deform), I conducted three pull groups on the COM (center of mass) of three domains of the protein. The pullings are all along the z axis but on

[gmx-users] PMF plot against distance

Dear Sir I have been working in umbrella sampling to analyse protein-ligand interaction and calculate Potential Mean Force (PMF). I have generated the following his.xvg file and have provided in the attachment. I request you to kindly guide me as to how to plot against distance. I also have the