[gmx-users] Announcement: release of FESetup 1.1

and parameterisation schemes. We particularly aim at automatisation where it makes sense and is possible, ease of use and robustness of the code. Please find the software at http://www.hecbiosim.ac.uk/repo/download/2-software/3-fesetup Kind regards, Hannes Loeffler. -- Gromacs Users mailing list * Please

Re: [gmx-users] difference of calculation time between the numbers of fep-lambdas values

On Mon, 27 Apr 2015 07:43:51 -0400 Justin Lemkul jalem...@vt.edu wrote: Note that without couple-moltype, you're going to be decoupling the whole system, which is (1) not what you want for calculating solvation free energy and (2) extremely slow. There is an inherent slowdown when running

Re: [gmx-users] difference of calculation time between the numbers of fep-lambdas values

On Mon, 27 Apr 2015 09:05:05 -0400 Justin Lemkul jalem...@vt.edu wrote: On 4/27/15 9:02 AM, Hannes Loeffler wrote: On Mon, 27 Apr 2015 07:43:51 -0400 Justin Lemkul jalem...@vt.edu wrote: Note that without couple-moltype, you're going to be decoupling the whole system, which is (1

Re: [gmx-users] Fwd: Bad performance in free energy calulations

Hi, somewhat off-topic but I wonder why in your free energy protocol you only vary the vdW and electrostatic lambdas. What about the others? Your mutation also transforms bonded terms and masses. One minor point is that your duplication of atomtypes (with i and m prefixes) seems pretty

Re: [gmx-users] Fwd: Bad performance in free energy calulations

On Tue, 19 May 2015 17:48:17 +0200 Julian Zachmann frankjulian.zachm...@uab.cat wrote: Concerning the changes of the atom types: the changes in the charges are really small and the results will probably be the same if I would not convert the whole ligand, just the 4 atoms which are changing.

Re: [gmx-users] Fwd: Bad performance in free energy calulations

On Tue, 19 May 2015 11:37:11 -0400 Michael Shirts mrshi...@gmail.com wrote: somewhat off-topic but I wonder why in your free energy protocol you only vary the vdW and electrostatic lambdas. What about the others? Your mutation also transforms bonded terms and masses. Minor point -

[gmx-users] [pairs] func type 2

Hi, do I interpret table 5.5 (Gromacs 4.6.7) correctly that function type 2 in section [pairs] can be used to realize mixed 1-4 scaling as it is necessary with mixing e.g. an AMBER protein force field with the GLYCAM force field? GLYCAM doesn't scale 1-4 interactions. Thanks, Hannes. --

Re: [gmx-users] Fwd: Bad performance in free energy calulations

see in the code and I think the manual says that too is that when couple-moltype is not set in the .mdp none of the other couple- parameters have any effect should I set any of the to something. Do I get this right? Many thanks for the answers, Hannes. On Tue, May 19, 2015 at 11:58 AM, Hannes

Re: [gmx-users] solvation free energy, electrostatic transformation

What happens when you do both transformations simultaneously, i.e. sc-coul=yes? On Mon, 27 Jul 2015 15:55:04 +0200 Daniele Veclani danielevecl...@gmail.com wrote: I'm trying to calculate the solvation free energy of a molecule (M). I have done a VdW. transformation. I have done also a

Re: [gmx-users] solvation free energy

The couple-* parameters take already care of including the non-bonded terms internal to your molecule to correctly describe the transfer of M to vacuum. That's the point of those parameters so that you would not have to run an additional correction in vacuo. See the discussion in the manual

Re: [gmx-users] solvation free energy

parameters. It's right? Of course, after the VdW I'll change the electrostatic transformation. Best regards D.V. 2015-07-16 16:55 GMT+02:00 Hannes Loeffler hannes.loeff...@stfc.ac.uk: The couple-* parameters take already care of including the non-bonded terms internal

Re: [gmx-users] Free energy calculations (FEP) and soft core potential 1-1-48

On Wed, 15 Jul 2015 16:20:25 +0200 Julian Zachmann frankjulian.zachm...@uab.cat wrote: The simulation time for 1ns is quite short of course but I have 'nstdhdl' put to 10 to get a lot of output. To add to what has been said already: increasing the output within a fixed set of time won't give

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

the couple-* switches as you suggested (attached), > but I am still receiving the same warning message: > "The lambda=0 and lambda=1 states for coupling are identical" > > I guess I am almost there, am I missing something else? > > Thanks again, > Sebastian > > >

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

me cg nr charge mass typeB chargeB massB 1 DU 1NA+ NA+ 1 0 22.9898 IP 0 22.9898 2 IM 1 DU DU2 0 35.4530 DU 0 35.4530 On Tue, 1 Dec 2015 13:17:38 +0000 Hannes Loeffler <hannes.loeff...@stfc.

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

Dear Sebastian, I have got your attachment. I do not know all intricacies of Gromacs but for relative free energies you only use one moleculetype for the perturbed group, see attachment. You do not use the couple-* switches for relative simulations. Yes, you are right about typeA and typeB.

Re: [gmx-users] support mmcif format?

On Mon, 23 Nov 2015 09:57:55 + Mark Abraham wrote: > I think we are unlikely to plan to write mmCIF directly as a > trajectory format, It's hard to see for me why someone would even want to use mmCIF as a trajectory format. The format serves, primarily, the

Re: [gmx-users] Software generating gaff for gromacs with am1bcc charges

On Fri, 3 Jun 2016 12:47:34 +0700 Andrian Saputra wrote: > Hi all, can anyone suggest me whats softwares can produce gaff > topology for gromacs with am1bcc charges automatically for 100-200 > atoms ? All the software I'm aware of wraps around antechamber and so won't do

Re: [gmx-users] Clarity on TI free energy terms

On Thu, 2 Jun 2016 08:27:15 + "Nash, Anthony" wrote: > Dear Hannes, > > Thanks for all the help yesterday, it helped. I, hopefully, have just > the one final question. > > I am still a little confused how Gromacs deals with the interactions > (vdW & Coul) with the

Re: [gmx-users] Clarity on TI free energy terms

On Wed, 1 Jun 2016 16:15:31 + "Nash, Anthony" wrote: > In the mean while, do you know of any tutorials (besides the methane > in water FE tutorial) regarding TI for amino acid substitution? I am not aware of one. You could try http://www.alchemistry.org/ > And by

Re: [gmx-users] Clarity on TI free energy terms

t an > example would be great)? > > Thanks > Anthony > > > On 01/06/2016 09:55, > "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of > Hannes Loeffler" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of hannes.loeff...@stfc.a

Re: [gmx-users] Clarity on TI free energy terms

On Wed, 1 Jun 2016 07:54:56 + "Nash, Anthony" wrote: > In the tutorial, charges are off in the topology and the electrostatic > coupling to lambda remains 0 throughout the 20 windows. I assume > setting col_lambdas=0 0 0 Š was for that very reason I.e., the > charges were

Re: [gmx-users] Clarity on TI free energy terms

On Wed, 1 Jun 2016 12:06:20 + "Nash, Anthony" wrote: > vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 > 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 > mass_lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 > 0.0 0.0 0.0

Re: [gmx-users] Clarity on TI free energy terms

On Wed, 1 Jun 2016 15:00:51 + "Nash, Anthony" wrote: > > This also assumes that > >you have vanishing atoms only. If you have appearing atoms only you > >would obviously have to revers the order, and when you have both you > >will have to run with two mdp/tpr setups. > >

Re: [gmx-users] refining a TI calculation - additional lambda points

On Tue, 26 Jan 2016 15:47:03 +0100 Oliwia Maria Szklarczyk wrote: > Dear All, > > I was wondering if you have tips on how to easily create additional > lambda points in a thermodynamic integration calculation in gromacs > 5. I have 21 lambda points already simulated, from L_0

Re: [gmx-users] Relative binding free energy

On Mon, 14 Mar 2016 14:08:32 + Stefania Evoli wrote: > Please, could you give a look at that? I obtained it by using the > useful tool described in the article 'A Python tool to set up > relative free energy calculations in GROMACS¹ Pavel V. Klimovich and > David

Re: [gmx-users] Relative binding free energy

> Post-Doctoral Fellow > King Abdullah University of Science and Technology > Catalysis center - Bldg. 3, 4th floor, 4231­WS18 > Thuwal, Kingdom of Saudi Arabia > stefania.ev...@kaust.edu.sa > > > > > > > On 3/14/16, 12:21 PM, > "gromacs.org_gmx-users-boun...@ma

Re: [gmx-users] Relative binding free energy

I had a quick look at this and I see quite a few problems there. You don't show the [atomtypes] but I suppose that whatever you call *_dummy has zero vdW parameters. BTW, there is no need to invent different atom type names for every dummy as their non-bonded parameters are all zero anyway and

Re: [gmx-users] Suggested settings for using Amber force field in Gromacs

On Thu, 5 May 2016 13:20:59 + "Casalini Tommaso" wrote: > Thanks a lot for your quick answer. > > I am trying to reproduce with Gromacs some results that I obtained > with Amber software. I put the same thermostat (Langevin) and > barostat (Berendsen with

Re: [gmx-users] Thermodynamic integration

A good starting point is http://www.alchemistry.org/ which has quite a lot of detail on relative alchemical free energy simulations (not only TI). On Mon, 18 Apr 2016 09:27:02 + "Nash, Anthony" wrote: > Hi all, > > I¹m looking for a guide on performing TI between a

Re: [gmx-users] Thermodynamic integration

ion of a side > >> chain.” > >> > >> I think this is what I am after. Many thanks for the link. > >> > >> Anthony > >> > >> > >> > >> On 18/04/2016 10:42, > >> "gromacs.org_gmx-users-boun...@maillist.sys.kth.

Re: [gmx-users] Moving this mailing list to Discourse format

rk > > On Thu, Apr 21, 2016 at 9:52 AM Hannes Loeffler > <hannes.loeff...@stfc.ac.uk> wrote: > > > On Thu, 21 Apr 2016 07:11:42 + > > Mark Abraham <mark.j.abra...@gmail.com> wrote: > > > > > Hi people, > > > > > > As part of t

Re: [gmx-users] Moving this mailing list to Discourse format

On Thu, 21 Apr 2016 07:11:42 + Mark Abraham wrote: > Hi people, > > As part of the new BioExcel project (http://bioexcel.eu/) that > supports biomolecular research with codes including GROMACS, we're > exploring migrating the gmx-users mailing list to the Discourse

[gmx-users] Release of FESetup 1.2

/?pagename=Releases Many thanks, Hannes Loeffler. -- 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 v

Re: [gmx-users] couple-moltype in FEP

On Tue, 12 Jul 2016 10:16:24 +0200 Alexander Alexander wrote: > Hi, > Thanks for your response. > I want to calculate the binding free energy of a single amino acid to > a solid surface in aqueous solution by FEP, alchemical > transformation, where perturbations

Re: [gmx-users] couple-moltype in FEP

On Tue, 12 Jul 2016 01:56:42 +0200 Alexander Alexander wrote: > I was wondering that how I can have for example two different > "couple-moltype" in free energy part of my *.mdp file in FEP, > alchemical transformation? The reason for having two is to perturb > each of

Re: [gmx-users] couple-moltype in FEP

On Tue, 12 Jul 2016 07:35:00 +0100 Hannes Loeffler <hannes.loeff...@stfc.ac.uk> wrote: > On Tue, 12 Jul 2016 01:56:42 +0200 > Alexander Alexander <alexanderwie...@gmail.com> wrote: > > > I was wondering that how I can have for example two different > > "cou

Re: [gmx-users] couple-moltype in FEP

On Tue, 12 Jul 2016 10:29:04 +0100 Hannes Loeffler <hannes.loeff...@stfc.ac.uk> wrote: > On Tue, 12 Jul 2016 10:16:24 +0200 > Alexander Alexander <alexanderwie...@gmail.com> wrote: > > > Hi, > > Thanks for your response. > > I want to calculate the bin

Re: [gmx-users] couple-moltype in FEP

On Tue, 12 Jul 2016 12:44:10 +0200 Alexander Alexander wrote: > Yes, Fig.6 comes from the different step in Fig.1. I think the > easiest way here is to have 6 different "topol-mdp" files > corresponding to each step. Although unlike the amino acid, defining > the [

Re: [gmx-users] The role of Jacobian factor in free energy simulations

Hi Stefano, you might be better off either inspecting the code yourself or contacting the developers directly (the Gromacs developer list may be open to this). Cheers, Hannes. On Mon, 12 Sep 2016 18:52:42 + BOSISIO Stefano wrote: > Dear Gromacs staff, > > I am

Re: [gmx-users] Gromacs Relative Free Energy Calculation Issue

On Wed, 5 Oct 2016 09:28:16 + Guanglin Kuang wrote: > Dear Hannes, > > Part I: > > I have tried to use FESetup to generate the topology/coordinate files > for the mutated ligands, but I met some problems. Also, I do not recognize anything in your archive file that has

Re: [gmx-users] Gromacs Relative Free Energy Calculation Issue

On Mon, 3 Oct 2016 19:57:07 + Guanglin Kuang wrote: > Dear Gromacs users, > > Has any of you managed to use Gromacs to do relative free energy > calculations? I have some technical questions that would need your > suggestions. > > I am trying to reproduce the Amber free

Re: [gmx-users] Free energy calculation problem with too high dG

On Tue, 4 Oct 2016 15:27:25 +0300 Vlad wrote: > I tried to do the decoupling and strangely the result is not the same > Below is the end of the log > The total dG is significantly less then previous and the last dG > value is particularly small I think total dG will get less

Re: [gmx-users] Free energy calculation problem with too high dG

On Tue, 4 Oct 2016 14:01:52 +0300 Vlad wrote: > No reason. I just thought it would give the same result. In theory both directions should be symmetrical and give the same result. > In the trajectory the ligand diffuse to the end of the cell like a > ghost through the

Re: [gmx-users] Free Energy of Binding Question

It usually helps to draw a thermodynamic cycle to inform yourself what exactly you are doing. What you seem to have been doing is to decouple the ligand, once from the WT and once from the MUT. This should give you the "absolute" binding free energy. Computing the difference between those

Re: [gmx-users] Free Energy of Binding Question

On Wed, 21 Sep 2016 12:00:29 + Abdülkadir KOÇAK wrote: > In terms of endstates, the state A is the real ligand complexed with > Protein in water... I did not define dummy atoms for the ligand as > the state B, which I believe I should have... I'm not quite sure what you

Re: [gmx-users] Free Energy of Binding Question

d states? See e.g. http://www.alchemistry.org/wiki/Example:_Absolute_Binding_Affinity > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > Hannes Loeffler <hannes.loeff...@stfc.ac.uk> Sent: Tues

Re: [gmx-users] Gromacs Relative Free Energy Calculation Issue

Hi, you could have a look into http://www.hecbiosim.ac.uk/fesetup to set up your system. It is late evening here so I will answer in more detail tomorrow. Cheers, Hannes. On Mon, 3 Oct 2016 19:57:07 + Guanglin Kuang wrote: > Dear Gromacs users, > > Has any of you

Re: [gmx-users] typeB in FEP calculations

On Tue, 27 Sep 2016 11:08:45 +0100 Rui Neves wrote: > However, what I would like to know is: > At the beggining of the topology I call for all the bonded terms > ('#include ffbonded.itp), and then in the [ atoms ] section, I > specify the massB, typeB and chargeB for the

Re: [gmx-users] MBAR issue

On Fri, 11 Nov 2016 09:04:35 +0100 gozde ergin wrote: > Dear all, > > I follow James Barnett tutorial of “Methane Free Energy of Solvation” > however I use betaine molecule other than methane. In order to > analyse the data I use alchemical_analysis.py code however I get

Re: [gmx-users] Free energy change and volume of the box

Have you had a look at http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme to see if that technique would be applicable to you and look through the references given? When you do absolute transformations you will need to think about standard state

Re: [gmx-users] Free energy - FEP

On Mon, 17 Oct 2016 18:06:01 +0200 Alex wrote: > What I have already done in Free energy simulation was to use the > output configuration of the last lambada windows as input > configuration (lambada_n.gro) for the new lambada windows and so on, > which this make

Re: [gmx-users] Adding FE2+ or FE3+ into the system

What are you planning to do with those parameters? You could have a look into the Li/Merz parameters (and papers!) available with the AmberTools (may not have been converted yet to Gromacs formats and the 12-6-4 sets would need support in the code). Generally, you should be wary when using simple

Re: [gmx-users] Adding FE2+ parameters

On Tue, 10 Jan 2017 12:19:15 -0500 Justin Lemkul wrote: > On 1/10/17 12:09 PM, CROUZY Serge 119222 wrote: > > Hello Hannes > > > > I'm perfectly aware how you need to be careful in using metal > > parameters - checking for which solvent and which coordination they > > have been

Re: [gmx-users] forward and backward states for the binding free energy energy

On Mon, 2 Jan 2017 14:17:56 +0300 Qasim Pars wrote: > 1-) The mean of the forward state is ~15 kcal/mol. That is too big, > right? Maybe the ligand doesn't get decoupled in the forward state? It will be hard to guess whether this is meaningful or not... You switch with 100

Re: [gmx-users] Continuing a FEP alchemical

On Wed, 28 Dec 2016 16:40:49 +0100 Alex wrote: > Hello Gromacs user, > > I have a free energy simulation converged results harvested by > alchemcial analysis in 15 lambada windows, now, I would like to > increase the number of lambada windows to 20. Would you please

Re: [gmx-users] Continuing a FEP alchemical

On Wed, 28 Dec 2016 17:24:08 +0100 Alex wrote: > Thank for your response. > > You mean for the TI analysis, now problem if one .xvg file (e.g. > case.3.xvg) has just 15 columns while another .xvg file (e.g. > case.18.xvg) has 20 columns? and still the "alchemical

Re: [gmx-users] query about structural consistency

On Tue, 21 Mar 2017 13:09:46 +0530 abhisek Mondal wrote: > Hi, > > I just have a basic query. > > I'm working with a protein-ligand system with a goal of performing > Umbrella sampling in gromacs. So first, after I build the complex, I'm > going for NVT and

Re: [gmx-users] Error in free energy calculation

I can't help you much because I have not really paid attention how restraints in alchemical free energy simulations are handled in newer versions of Gromacs. I understand that [intermolecular_interactions] is a new section that allows using restraints based on global indices. The error message

Re: [gmx-users] Error in free energy calculation

On Thu, 16 Mar 2017 10:09:58 + Vytautas Rakeviius wrote: > You should try to add PLUMED (plumed.org) to GROMACS for such > things.Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, > D., Raiteri, P., ... & Parrinello, M. (2009). PLUMED: A portable > plugin

Re: [gmx-users] Alchemical free energy

On Tue, 4 Apr 2017 18:57:50 +0200 Alex wrote: > In relative binding free energy calculation via alchemical free > energy, I noticed that either the word "Decouple" or "Annihilate" is > used. What is the difference between them? Actually, this is typically used in the

Re: [gmx-users] Fwd: Relative free energy perturbation

; Date: Mon, 26 Jun 2017 12:09:45 +0100 > > From: Hannes Loeffler <hannes.loeff...@stfc.ac.uk> > > To: <gromacs.org_gmx-users@maillist.sys.kth.se> > > Cc: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Fwd: Relative free energy perturbation > > Message-I

Re: [gmx-users] Perturbation Thermodynamic Integration

I have not really followed the previous email exchange but from this mdp file I wonder what you are trying to achieve. You seem to want to decouple all atoms of your HEPT molecule (couple-moltype, couple-intramol) from its environment but then you also change the masses. What is the physical

Re: [gmx-users] Perturbation Thermodynamic Integration

On Tue, 16 May 2017 10:28:08 -0400 Dan Gil wrote: > Thank you for the advice on the cut-off schemes and PME methods. > > What is the physical meaning of a non-interacting final state > > that has different masses from the initial state? > > > These free energy options

Re: [gmx-users] Fwd: Relative free energy perturbation

On Mon, 26 Jun 2017 12:25:19 +0200 Davide Bonanni wrote: > 1) Can I perform the calculation in a single step with soft core > potential enabled? I mean, is it correct to transform directly the > hydrogen into a chlorine instead of using 2 topologys and 2 > complexes,

Re: [gmx-users] Perturbation Thermodynamic Integration

On Tue, 16 May 2017 15:13:10 -0400 Dan Gil wrote: > If you do this via decoupling ("absolute" transformation) you do that > > once for molecule A and once for molecule B. > > > I believe you are referring to the BAR method? I am trying to see if > I get the same

Re: [gmx-users] Perturbation Thermodynamic Integration

26 0.030 0.0 > 6978.993 1.390 352.654 7972.572 0.000 151.629 0.000 154.128 0.000 0.1 > 2160.691 4.261 219.874 7020.561 0.000 94.026 0.000 96.219 0.263 0.2 > 301.074 32.826 249.228 7137.750 0.000 78.224 0.000 80.446 0.002 0.3 > 694.265 1.765 123.119 7225.511 0.000 80.863 0.000 83.117 0

Re: [gmx-users] Increasing sigma

On Fri, 5 May 2017 15:09:09 +0200 Pallavi Banerjee wrote: > I intend to perform thermodynamic integration of my system, but not to > calculate the free energy. I want to gradually increase the radius of > the carbon atoms of the alkyl chains of my lipid