[gmx-users] free energy

Dear gmx-usersI want to calculate free energy of binding of ligand to Au surface in 8 ns simulation. I considered 7 lambda (lambda= 0, 0.2, 0.4, 0.6, 0.8, 0.9, 1) and for every lambda a mdp file. for example lambda-0 mdp file: title   =  n.pdb restraining cpp =  /lib/c

[gmx-users] Free energy

Dear Justin,I studied your tutorial entitle "Free Energy Calculations: Methane in Water", Is it based on Thermodynamic integration (TI) methods? I want to know how to calculated free energy based on perturbation theory? I have a drug with a carrier at water medium and I want to calculate free en

[gmx-users] free energy calculation

Dear users For calculating free energy of methan (in justin tutorial) I changed important parameters instead of the parameters in lambda=0 that having in that tutorial Is it correct? Or i must create those files by this command: Perl write_mdp.pl em_steep.mdp for every lambda?! I did this way.bu

[gmx-users] free energy problem

Dear Justin thanks for your replys and your patient i think my main problem is the way of using of perl/shell scripts in your tutorial (Free energy for methane) my question is: for script using, i must be execute them by *(chmod +x ...) * and then use of this command (*perl write_mdp.pl

[gmx-users] free energy question

Dear Justin Your mean is, i should use: perl write_mdp.pl em_steep.mdp For creating *.mdp files for EM process per lambdas And for producing for example nvt.mdp,i must write: perl write_mdp.pl nvt.mdp ? Also for acheiving neccesary files for run process we need to shell files ...but i dont know

[gmx-users] free energy calculation

hello gromacs users i am working on protein complex with popc membrane i want to calculate the free energy of complex i have run protein complex and dppc tutorial how to start for that i am using 4.5 version of gromacs should i use GROMACS Tutorial Free Energy Calculations: Methane in Water ki

[gmx-users] Free Energy calculation

hello gromacs users i am working on protein ligand complex with popc membrane i want to calculate the free energy of protein and ligand i have to follow which tutorial (methane in water) but my protein is membrane protein i am also running md simulation (70 ns) i am new in free energy calculation

[gmx-users] free energy calculations

Dear Gromac's users, I'd like to perform a FEP calculations. I've done yours tutorial and now follow by it, i'd like to perform my calculations for small molecule in water. I got a problem: Fatal error: No such moleculetype SOL I don't know what it means in these cases, because both files are sim

[gmx-users] free energy calculator

Dear Gromacs Users, We have constructed a free-energy calculator of bonded potential terms according to the article: A. Farhi and B. Singh, New J. Phys. 18, 023039, 2016. The calculations are in principle immediate and take few seconds through the website. https://www.wolframcloud.com/obje

[gmx-users] free energy calculator

Dear Gromacs Users, We have constructed a free-energy calculator of bonded potential terms according to the article: A. Farhi and B. Singh, New J. Phys. 18, 023039, 2016. The calculations are in principle immediate and take few seconds through the website. https://www.wolframcloud.com/obje

[gmx-users] Free Energy calculatio

Dear gromacs users, I want to do Gibbs Free energy calculations. In my case their are two molecule in PDB file. I have generated topology file by TopolGen-1.1. Now got the error like Syntax error - File structure.top, line 10 Last line read: '[ moleculetype ]' Invalid order for directive moleculet

[gmx-users] free energy landscape

​HI there I got free energy landscape using Mathematica software to get coordinates with the least free energy. 3d image of the landscape shows a gap though!? would that be reliable to get coordinates from any point on the lowest energy coordinate ? any recommendation would be appreciated Pakr

[gmx-users] free energy calculation.

Hi! Dear gmx users, I have md simmulations of a protein with four different ligands. now I want to calculate the free energy of binding. which method does suit after md simmulation? either g_mmpbsa or gmx BAR method. If I use BAR method is it necessary to set charges to zero as in the tutorial g

Re: [gmx-users] free energy

On 4/26/15 8:54 AM, fatemeh ramezani wrote: Dear gmx-usersI want to calculate free energy of binding of ligand to Au surface in 8 ns simulation. I considered 7 lambda (lambda= 0, 0.2, 0.4, 0.6, 0.8, 0.9, 1) and for every lambda a mdp file. for example lambda-0 mdp file: title =

[gmx-users] free energy binding

Dear A. Lemkul I'm writing about the problem with the calculation of free energy binding. I used 20 steps for the calculation of the free energy, only three of these steps (7,12,19) I find this error. And in these steps simulation terminates prematurely. Best regards -- Gromacs Users mailing l

[gmx-users] free energy binding

Dear A. Lemkul I'm writing about the problem with the calculation of free energy binding. I used 20 steps for the calculation of the free energy, only three of these steps (7,12,19) I find this error. And in these steps simulation terminates prematurely. Best regards -- Gromacs Users mailing l

[gmx-users] Free energy calculation

Dear all I'm trying to calculate free energy of solvation according to Justin's tutorial for my protein in water. Is it true to follow that tutorial for my protein? any special changes in MDP file is necessary ? If there is no differences for systems to calculate free energy of solvation accordi

[gmx-users] Free Energy Calculations

Hi Everyone, I use ancient version of Gromacs 4.5.5 for free energy calculations. I have two different questions. 1) When I run g_bar for results, I get this lambda 0.000 - 0.050, DG -2.16 +/- 0.00 lambda 0.050 - 0.100, DG -2.16 +/- 0.01 lambda 0.100 - 0.150, DG -2.09 +/- 0.01 lamb

[gmx-users] Free Energy Calculation

Dear Sir I have been calculating free energy of molecular solid based on recent work by J.L. Aragones, E.G. Noya, C. Valeriani and C. Vega (J. Chem. Phys. 139, 034104 (2013)) I am calculating it for methanol. My .mdp file for production run is as follows title= EM alpha methano

[gmx-users] Free energy landscpae

Hello users and experts I have performed a protein-ligand simulation with Gromos 43a1 ff and SPC water model. I performed PCA and selected first 2 principal components for construction of FEL using gmx sham. However, from the available references i have seen that the there exist both positive and n

[gmx-users] Free energy - FEP

Dear gromacs user, 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 simulation so time demanding as one lambada should start after the oth

[gmx-users] Free energy change

Dear gromacs user, I have calculated the free energy change of a charged molecule in box1, but now, I need to do it again but in a bigger box. Box1: (a1, b1, c1) and number of water molecules: N1 Box2: (a2, b2, c2) and number of water molecules: N2 To avoid the second simulation, I was wondering

[gmx-users] Free energy calculation

Dear Gromacs users, I have a system of protein-protein interaction. Is it possible to calculate the free energy of the complex? If it so, could you please give me an efficient tool to compute the free energy calculation. Any suggestion. Thank you *Khadija AMINE* *Computational Biology* *Pos

[gmx-users] free energy settings

Dear users, I have a few questions about the below free energy settings: ;State A free-energy = yes init-lambda = 0 delta-lambda = 0 sc-alpha = 0.5 sc-power = 1 sc-sigma = 0.3 couple-intramol = no coupl

[gmx-users] Free energy calculations

Hello gmx-users I wanted to compute binding free energy for a protein-ligand complex by gromacs. I sued MM/PBSA approach http://rashmikumari.github.io/g_mmpbsa/ but here the entropic terms could not be computed which is the backbone limitation to restrict the actual free energy determination. P

[gmx-users] Free energy calculation

Hi All, I am interested to calculate the free energy of coarse-grained lipid monolayer which contains CG lipid, cholesterol, water and nanoparticles. Any suggestions regarding Metadynamics or Umbrella sampling? Any tutorial that will be helpful for learning? I am trying Metadynamics learning with

[gmx-users] Free energy calculation

Dear gmx user I am working on protein ionic liquid interaction. I am trying to calculate the binding free energy of ionic liquid (system contain ~ 100 ionic liquid molecule). Is there any way to calculate the binding free energy in pre processing stage of post processing stage. *

[gmx-users] Free energy calculation

Dear gmx user I am working on protein ionic liquid interaction. I am trying to calculate the binding free energy of ionic liquid (system contain ~ 100 ionic liquid molecule). Is there any way to calculate the binding free energy in pre processing stage of post processing stage. -- Gromacs

[gmx-users] Free Energy code

Dear all, I am quite new to free energy calculation, so I apologize if the questions seem naive and of course they are a lot. My intention is to turn off vdw and coulombic interactions to perform some tempering cycles on my system. There are though some questions: 1- I only want to decou

[gmx-users] Free energy landscape

Hi users I find few methods of plotting free energy landscape. Of them one is plotting rg vs rmsd and another one is using Principe components. What is the difference in these two methods? Is the plot obtained by both the method are one and the same? Thank you -- Gromacs Users mailing list * Pl

[gmx-users] free energy landscape

Dear, i want to make a free energy landscape with respect to Rg and RMSD. First i get the rmsd.xvg by g_rms and then get the Rg.xvg file by g_gyrate. And the i merge the rmsd value and Rg value into one file with two column, then i use the g_sham command to got the free energy landscapes. do

[gmx-users] free energy calculations

three questions regarding free energy calculations ... 1) i try running a free energy calculation and get an error msg: "The Verlet cut-off scheme does not (yet) support free-energy calculations with perturbed atoms, only perturbed interactions. This will be implemented soon. Use the group schem

[gmx-users] Free energy calculation of

Dear gxm users, Now I am doing solvation free energy of a protein, I follow Sander Pronk's tutorial downloaded from Gromacs page. 1. How do I check system is equilibrated? 2. I run following command sh mklambdas.sh run.mdp topol.top equil.gro I got following error: mklambdas.sh: 12: mklam

[gmx-users] free energy of methan

Dear users in attached *.mdp* file, if i replaced *init_lambda_state=0.05 , 0.1 , 0.15* , ... instead of *0* for* lambda=0* is correct? i didnot see foreign lambda in this mdp file.where i include foreign lambda??? regards elham tazikeh *mdp file for lambda=0* ; Free energy control stuff f

Re: [gmx-users] free energy calculation

On 10/16/14 5:02 AM, elham tazikeh wrote: Dear users For calculating free energy of methan (in justin tutorial) I changed important parameters instead of the parameters in lambda=0 that having in that tutorial Is it correct? If you're trying to execute the tutorial, no, don't make any chang

[gmx-users] free energy for ethanol

Dear Justin i really appriciate for your reply i trying to follow this tuturial about free energy of ethanol: *http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf * there was* mklambda.sh* in that tutorial when i used ab

Re: [gmx-users] free energy problem

On 10/19/14 5:14 AM, elham tazikeh wrote: Dear Justin thanks for your replys and your patient i think my main problem is the way of using of perl/shell scripts in your tutorial (Free energy for methane) my question is: for script using, i must be execute them by *(chmod +x ...) * and then us

Re: [gmx-users] free energy question

On 10/19/14 11:31 PM, elham tazikeh wrote: Dear Justin Your mean is, i should use: perl write_mdp.pl em_steep.mdp For creating *.mdp files for EM process per lambdas And for producing for example nvt.mdp,i must write: perl write_mdp.pl nvt.mdp ? Yes, which is exactly what is stated on htt

Re: [gmx-users] free energy calculation

On 10/20/14 6:16 AM, RINU KHATTRI wrote: hello gromacs users i am working on protein complex with popc membrane i want to calculate the free energy of complex i have run protein complex and dppc tutorial how to start for that i am using 4.5 version of gromacs should i use GROMACS Tutorial F

Re: [gmx-users] Free Energy calculation

On 11/13/14 4:09 AM, RINU KHATTRI wrote: hello gromacs users i am working on protein ligand complex with popc membrane i want to calculate the free energy of protein and ligand i have to follow which tutorial (methane in water) but my protein is membrane protein i am also running md simulation

Re: [gmx-users] Free Energy calculation

Thank you justin is there any tutorial like kalp in dppc which i can follow how can i calculate the diffusion coefficient of ligand(drug) thanks in advance On Fri, Nov 14, 2014 at 12:04 AM, Justin Lemkul wrote: > > > On 11/13/14 4:09 AM, RINU KHATTRI wrote: >> >> hello gromacs users i am working

Re: [gmx-users] Free Energy calculation

On 11/18/14 11:46 PM, RINU KHATTRI wrote: Thank you justin is there any tutorial like kalp in dppc which i can follow how can i calculate the diffusion coefficient of ligand(drug) thanks in advance You can calculate diffusion coefficients with g_msd. -Justin On Fri, Nov 14, 2014 at 12:04

Re: [gmx-users] free energy calculations

On 1/29/16 7:27 AM, Marta Wisniewska wrote: Dear Gromac's users, I'd like to perform a FEP calculations. I've done yours tutorial and now follow by it, i'd like to perform my calculations for small molecule in water. I got a problem: Fatal error: No such moleculetype SOL I don't know what it

Re: [gmx-users] free energy calculations

Dear Marta, Probably you forgot to put the line regarding the topology of the water into the topology file of your system. #include "amber99sb.ff/tip3p.itp² (for example) Stefania ‹Dr. Stefania Evoli Post-Doctoral Fellow King Abdullah University of Science and Technology Catalysis center - Bl

Re: [gmx-users] Free Energy calculatio

Hi, Your error message is simple to resolve, if you include your moleculetype directives in the right order (see reference manual). But I cannot understand your real objective. Mark On Sun, Apr 15, 2018, 11:21 Anjali Patel wrote: > Dear gromacs users, > > I want to do Gibbs Free energy calcula

Re: [gmx-users] Free Energy calculation

Hello, Thank you for the quick reply @ Mark Abraham. I am describing in detail what i want to do. I have taken SWCNT (12*12)and encapsulate the molecule. Now i want to check its binding free energy. I checked reference manual to arrange the right order but didn’t success. can anyone have any other

Re: [gmx-users] free energy landscape

Sounds like a problem for string methods. However, it's hard to judge without actually looking at what you have. Cheers. On Sun, May 13, 2018 at 3:47 PM Rezgar Pakravan wrote: > ​HI there > > I got free energy landscape using Mathematica software to get coordinates > with the least free energy.

[gmx-users] free energy of restraints

Dear Gromacs Users, Hi, we have added a free energy calculation of a dihedral restraint to the free energy website. Now it has exact analytical free energy calculations of all the restraints (can be used in absolute free energy calculations) and the standard bonded terms https://www.wolf

[gmx-users] free energy binding problem

Dear Useres I am studying an antibiotic in water (box with antibiotic and 1000 molecules of water), I am currently doing a calculation of free energy binding. My problem is that, for some values of lambda, I have this error: Step 1447079, time 2894.16 (ps) LINCS WARNING relative constraint devia

Re: [gmx-users] free energy binding

On 6/4/15 8:41 AM, Daniele Veclani wrote: Dear A. Lemkul I'm writing about the problem with the calculation of free energy binding. I used 20 steps for the calculation of the free energy, only three of these steps (7,12,19) I find this error. And in these steps simulation terminates prematur

Re: [gmx-users] Free energy calculation

On 6/22/15 5:53 AM, nazli kashani javid wrote: Dear all I'm trying to calculate free energy of solvation according to Justin's tutorial for my protein in water. Is it true to follow that tutorial for my protein? any special changes in MDP file is necessary ? You shouldn't use this method a

Re: [gmx-users] Free energy calculation

thanks for your clear answer. Is there any reasonable method for calculating free energy of solvation for my protein? :-( On Mon, Jun 22, 2015 at 2:26 PM, Justin Lemkul wrote: > > > On 6/22/15 5:53 AM, nazli kashani javid wrote: > >> Dear all >> >> I'm trying to calculate free energy of sol

Re: [gmx-users] Free energy calculation

I'm trying to show thermodynamic stabilities of my protein from free energy simulation. And I chose free energy of solvation, so if I can't use this method how can I show thermodynamic stabilities of my protein? On Mon, Jun 22, 2015 at 3:40 PM, nazli kashani javid wrote: > thanks for your clea

Re: [gmx-users] Free energy calculation

On 6/22/15 7:10 AM, nazli kashani javid wrote: thanks for your clear answer. Is there any reasonable method for calculating free energy of solvation for my protein? :-( Try MM/PBSA or MM/GBSA calculations. -Justin -- == Justin A. Lemkul, Ph

Re: [gmx-users] Free Energy Calculations

On 7/17/15 3:35 AM, Live King wrote: Hi Everyone, I use ancient version of Gromacs 4.5.5 for free energy calculations. I have two different questions. 1) When I run g_bar for results, I get this lambda 0.000 - 0.050, DG -2.16 +/- 0.00 lambda 0.050 - 0.100, DG -2.16 +/- 0.01 lambda

[gmx-users] Free energy calculation - parallelization

Hi, I have a question concerning the parallelization capabilities of Gromacs (>=v5.0.5) for free energy calculations. My computer specifications are 2xIntel® Core™ i7-4790K (2x4 cores) and 2x NVIDIA Tesla k20. Reading part of the manual, I know that gromacs will offload the nonbonded forces (

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 simulation so time demanding as o

Re: [gmx-users] Free energy calculation

It would probably be easiest to generate a PMF curve. Try Justin Lemkul's PMF tutorial and alter the box geometry as needed... :) On 28 November 2016 at 20:56, Khadija Amine wrote: > Dear Gromacs users, > > I have a system of protein-protein interaction. > > Is it possible to calculate the free

Re: [gmx-users] Free energy calculation

Thank you Williams. I should try the umbrella sampling tutorial? My complex is simulated during 20ns. The starting files for free energy computing should be the MD production files? *Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* On Mon

Re: [gmx-users] Free energy calculation

On 11/28/16 8:02 AM, Khadija Amine wrote: Thank you Williams. I should try the umbrella sampling tutorial? My complex is simulated during 20ns. The starting files for free energy computing should be the MD production files? Free energy of what? The tutorial suggested before is useful for

Re: [gmx-users] Free energy calculation

As I have mentioned in my first email, I want to calculate the free energy of my protein-protein complex. I want to compute free energies for wild type and mutant complex and compare them. *Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* On

Re: [gmx-users] Free energy calculation

On 11/28/16 8:56 AM, Khadija Amine wrote: As I have mentioned in my first email, I want to calculate the free energy of my protein-protein complex. That can be a bit ambiguous. I want to compute free energies for wild type and mutant complex and compare them. This is a more clearly defin

Re: [gmx-users] Free energy calculation

Could you please propound a suggestion more helpful for doing it? Should I perform more MD simulation for my complexes? *Khadija AMINE* *Computational Biology* *Postdoctoral Research Associate* *Carnegie Mellon University* On Mon, Nov 28, 2016 at 4:56 PM, Khadija Amine wrote: > As I have men

Re: [gmx-users] Free energy calculation

On 11/28/16 9:22 AM, Khadija Amine wrote: Could you please propound a suggestion more helpful for doing it? MM/PBSA calculations use the MM energy and solvation free energy estimates from PB to give the free energy of a given conformation. Combined with entropy calculations (Schlitter or

Re: [gmx-users] free energy settings

On 12/4/16 3:09 PM, Qasim Pars wrote: Dear users, I have a few questions about the below free energy settings: ;State A free-energy = yes init-lambda = 0 delta-lambda = 0 sc-alpha = 0.5 sc-power = 1 sc-sigma

[gmx-users] Free Energy Landscape- PCA

Hi everyone, I have a number of trajectories over which I have conducted PCA using Gromacs. I have also generated a Free Energy Landscape using g_sham when the trajectory is projected along the PCs. I would like to know how I can extract the coordinates of those states of minimum energy shown

[gmx-users] Free Energy Landscape- PCA

Hi everyone, I have a number of trajectories over which I have conducted PCA using Gromacs. I have also generated a Free Energy Landscape using g_sham when the trajectory is projected along the PCs. I would like to know how I can extract the coordinates of those states of minimum energy show

Re: [gmx-users] Free energy calculations

Hi, There's a very large literature on binding free energy calculations, and most of the methods can be implemented in GROMACS. Mark On Thu, 2 Mar 2017 06:50 Amir Zeb wrote: > Hello gmx-users > > I wanted to compute binding free energy for a protein-ligand complex by > gromacs. I sued MM/PBSA

Re: [gmx-users] Free energy calculation

You don't have a well-posed scientific question yet. Come back when you've thought about the hypotheses you want to test, and have written out what you are planning to do. Try to do the calculations yourself, and come back if they are not working. This is a help discussion forum for people who a

Re: [gmx-users] Free energy calculation

Hi Michael, Thank you for your valuable advice. Regards Imamul Sincerely Your’s *Sheikh Imamul Hossain* PhD Research Student Mechanical Engineering | School of Chemistry, Physics and Mechanical Engineering | Faculty of Science and Engineering | Queensland University of Technology| 2 George St Br

Re: [gmx-users] free energy landscape

On 11/28/13 7:20 AM, aixintiankong wrote: Dear, i want to make a free energy landscape with respect to Rg and RMSD. First i get the rmsd.xvg by g_rms and then get the Rg.xvg file by g_gyrate. And the i merge the rmsd value and Rg value into one file with two column, then i use the g_sham comman

[gmx-users] free energy caculation error

Hi all, I want to caculate the free energy of a molecule, but when I run the MD, it appears the error: "There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 4.4 nm. Change the number of nodes or mdrun option -rdd or -dds".However, even th

[gmx-users] Free energy change calculation

Hi, Sorry to bother you. Recently, I have encountered a problem when running free energy calculation of a dna-ligand complex system. The structure start to getting weird when I try to specify the two state (A,B) in the topology file, which is never spotted in the unconstrained MD simulations.

[gmx-users] Free energy of protonation

Dear list, I am trying to calculate the free energy for protonating a single monomer of oleic acid with the martini forcefield. This in preparation for other work, and I wanted to start by reproducing what is already done. To do this, I have defined the following in my topology to describe the ch

[gmx-users] free energy calculation for methane

Dear Justin thanks for your reply i trying to follow your tutorial but when i want to produce neccesary files per lambdas by this command: Perl write_mdp.pl em_steep.mdp i received 20 files as i expected but they are empty, for this reason i try to change some important parameters in your mdp file

Re: [gmx-users] free energy for ethanol

On 10/18/14 1:38 AM, elham tazikeh wrote: Dear Justin i really appriciate for your reply i trying to follow this tuturial about free energy of ethanol: *http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf * there was

[gmx-users] Free energy in implicit solvent

Dear gromacs users, Is it possible to calculate free energy in implicit solvent in gromacs? -- 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 *

[gmx-users] Free energy calculation by MM_PBSA

Hello everyone, I am trying to calculate free energy of protein ligand complex by using MM_PBSA method. While calculating polar solvation energy of the complex, I am getting this error. * Segmentation fault (core dumped).* *Please help!* With regards, Indu -- Gromacs Users mailing list * Pleas

[gmx-users] free energy of mutated protein

Hi! I wanted to see the effect of mutations on a protein. So I mutated the protein using chimera and then calculated the potential energy and all using Gromacs. Is there a command, after the energy equilibration step, that I can use to find the free energy? -- Regards, Raag -- Gromacs Users ma

[gmx-users] Free energy: sum or average

Upon free energy calculations via continuous decoupling, free-energy = yes couple-moltype = MOL couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = no init-lambda = 1.0 delta-lambda = -4e-8 sc-alpha

[gmx-users] Free energy - Methane in water

Dear gromacs user, In Free energy calculation tutorial of Methane in water, two energy minimization steps are done in order, first the steepest descents one where the rigid structures are used and then L-BFGS in which the flexible structure is used in (define = -DFLEXIBLE). My question is: in a tw

[gmx-users] free energy of complex system

Hi, I'm just trying to calculate free energy of a complex system using following method: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html However, I'm facing some difficulties understanding how can I achieve the goal. The tutorial goes on with a s

Re: [gmx-users] free energy binding problem

On 6/4/15 4:38 AM, Daniele Veclani wrote: Dear Useres I am studying an antibiotic in water (box with antibiotic and 1000 molecules of water), I am currently doing a calculation of free energy binding. My problem is that, for some values of lambda, I have this error: Step 1447079, time 2894.16

[gmx-users] Free energy calculation for aminoacids

Hi all I want to calculate free energy of solvation for a leucine and some other aminoacids individually,according to Justin tutorial : methane in the water. Is it reasonable to follow that method for free energy determination of one amino acid? Cheers -- Gromacs Users mailing list * Pleas

[gmx-users] Free energy calculation for aminoacids

Hi all I want to calculate free energy of solvation for a leucine and some other aminoacids individually,according to Justin tutorial : methane in the water. Is it reasonable to follow that method for free energy determination of one amino acid? Cheers body {height: 100%; color:#00; fo

[gmx-users] Free Energy of Liquid Water

Hi everyone, I would like to use Gromacs to do Thermodynamic Integration (TI) from liquid water (TIP4P model) to an ideal gas, to find the relative free energy. To do this, I believe one generally integrates above the critical point by increasing the temperature above the critical temperature

[gmx-users] Free Energy of Binding Question

Dear GMX Community, I am aiming to compare the relative binding energy (BE) of a ligand to wild type (WT) vs mutant (MUT) protein and thus trying to run a Free Energy Calculation for the binding energy of the ligand to both proteins (WT and MUT) using Bennett Acceptance Ratio (BAR). As the fir

[gmx-users] Free Energy of Binding Question

Dear GMX Community, I am aiming to compare the relative binding energy (BE) of a ligand to wild type (WT) vs mutant (MUT) protein and thus trying to run a Free Energy Calculation for the binding energy of the ligand to both proteins (WT and MUT) using Bennett Acceptance Ratio (BAR). As the fir

[gmx-users] Free energy calculations with membrane

Hi everyone, I am trying to do Justin's thermodynamic integration tutorial with a lipid bilayer. I believe the energy I will get from this exercise is the energy required to take alanine from membrane to vacuum. I have placed my alanine at the center of bilayer. Does this energy output contain con

Re: [gmx-users] Free Energy Landscape- PCA

On 12/12/16 9:30 AM, Romero, Raquel wrote: Hi everyone, I have a number of trajectories over which I have conducted PCA using Gromacs. I have also generated a Free Energy Landscape using g_sham when the trajectory is projected along the PCs. I would like to know how I can extract the coord

Re: [gmx-users] Free Energy Landscape- PCA

Thanks a lot for your reply, Justin. That’s exactly what want but my problem is that don’t know how, I mean, how can I know that correspondence? Getting that correspondence is my only problem > On 14 Dec 2016, at 12:49, Justin Lemkul wrote: > > > > On 12/12/16 9:30 AM, Romero, Raquel wrot

Re: [gmx-users] Free Energy Landscape- PCA

On 12/15/16 10:02 AM, Romero, Raquel wrote: Thanks a lot for your reply, Justin. That’s exactly what want but my problem is that don’t know how, I mean, how can I know that correspondence? Getting that correspondence is my only problem You (presumably) constructed a time series of eigenvalu

Re: [gmx-users] Free Energy Landscape- PCA

Thanks a lot, I know how to do it now, so each value given in the 2dproj.xvg corresponds to a time step of the simulation, right? so if I delimit the area in the FEL of which I want to know the coordinates i can extract all the frames that correspond to those eigenvalues by searching in the fil

Re: [gmx-users] Free Energy Landscape- PCA

Hi, The trjconv -drop* functionality is useful here. IIRC it only does a 1D form, but you can do two stages of that. Mark On Fri, 16 Dec 2016 02:36 Romero, Raquel wrote: > Thanks a lot, I know how to do it now, so each value given in the > 2dproj.xvg corresponds to a time step of the simulatio

[gmx-users] free energy calculation for histone

Dear all users, I am new for using GROMACS. and also read the tutorial of Methane and water. I have already simulated data of 100 ns for four histones. I want to know how to calculate free energy solvation from this data. which topology file and coordinate files I will use? I will appreciate you

[gmx-users] Free energy calculation of Histone

Dear all users, I am new for using GROMACS. and also read the tutorial of Methane and water. I have already simulated data of 100 ns for four histones. I want to know how to calculate free energy solvation from this data. which topology file and coordinate files I will use? I will appreciate you

[gmx-users] free energy perturbation segmentation fault.

Dear GROMACS users, I am trying to perform a perturbation of a valine Ac-VAL-NHMe into an alanine Ac-ALA-NHMe. Recently I have posted on the gromacs mailing list [Free energy perturbation parameters sc-alpha sc-power sc-sigma ] as I was experiencing problems (LINCS warning and crashes) in equilibr

[gmx-users] Free energy calculation problems (bug?)

Dear GROMACS users! I've encountered a problem in thermodynamic integration with GROMACS. I'm interested in calculating of solvation free energy differences between holbenzenes and benzene. To calculate this values I use thermodynamic integration approach (5 point formula). Half a year ago I did

Re: [gmx-users] free energy caculation error

lmgtfy: http://bit.ly/1lJYVGQ ;) -- Szilárd On Wed, Apr 9, 2014 at 12:41 PM, jane <348363...@qq.com> wrote: > Hi all, > I want to caculate the free energy of a molecule, but when I run the MD, it > appears the error: "There is no domain decomposition for 8 nodes that is > compatible with the give

Re: [gmx-users] free energy caculation error

On 4/9/14, 6:41 AM, jane wrote: Hi all, I want to caculate the free energy of a molecule, but when I run the MD, it appears the error: "There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 4.4 nm. Change the number of nodes or mdrun o

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