Re: [gmx-users] free energy

Dear Kiana, You can contact with Paissoni Cristina (email: paissoni.crist...@hsr.it) to get tool using MM/PBSA with GROMACS. Hope it help :) Cheers, Kieu Thu On Tue, Nov 5, 2013 at 7:18 PM, Justin Lemkul wrote: > > > On 11/5/13 3:45 AM, kiana moghaddam wrote: > >> Dear GMX Users >> >> >> >> I

Re: [gmx-users] free energy

On 11/5/13 3:45 AM, kiana moghaddam wrote: Dear GMX Users I am using parmbsc0 force field to study DNA-ligand interaction but my problem is free energy calculation (MMPBSA) for this interaction. How can I calculate free energy using MMPBSA approach? Thank you very much for your time and c

Re: [gmx-users] Free Energy Calculations in Parallel

On 7/26/13 4:06 PM, Quintin Sheridan wrote: Dear Gromacs Users, Is it possible to run free energy calculations in parallel using mpirun? If Yes, the free energy code is parallelized, either via MPI or threads. not I am wondering what the fastest way to run a free energy calculation is. I a

Re: [gmx-users] free energy calculations of methane in water computed by GMX ver 4.5.7 and ver 4.6.2

On 6/21/13 11:07 AM, Dwey wrote: Hi gmx-users, I almost reproduced free energy calculations of methane in water on Justin's website. First of all, I am able to follow the workflow of computing solvation free energy for several times with Gromacs version 4.5.7 and version 4.6.2 install

Re: [gmx-users] Free energy calculation: merge the topology of 2 molecules

Thanks for your reply, Stephan. Did the molecule you worked with have any atoms that are isolated (non-bonded) to the others? Was the equilibration run in your 1st case just a way to recruit those isolated atoms to the others in the same molecule? I suspect I might need to add artificial bond to c

Re: [gmx-users] free energy of system

On 4/25/13 12:02 PM, sarah k wrote: Dear all, I'm interested in calculating the Gibbs free energy of some systems. I have several questions in this regard: 1- The g_energy command gives some values in kJ/mol for total energy and enthalpy. Does the reported total energy include entropy effects

Re: [gmx-users] Free Energy Calculations in Gromacs

Thank you Professor Shirts. So now my protein itp file looks like this: [ atoms ] ; nrtype resnr residue atom cgnr chargemasstypeB chargeB MassB 1 CT1ACECH3 1 -0.190264 12.01 CT_per -0.12033412.01 [ bonds ] ;ai aj func th0 kb th0

Re: [gmx-users] Free Energy Calculations in Gromacs

You have to change atom types. For example: [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon h1h1 0. 0. A 2.47135e-01 6.56888e-02 h1_pert h1 0. 0. A 2.47135e-01 3.56888e-02 ; perturbed The

Re: [gmx-users] Free energy on GPU?

On 4/18/13 2:30 PM, Олег Титов wrote: Dear all. I'm trying to estimate relative solvation enegry of brombenzene (relative to benzene) via thermodynamic integration. Can I perform such calculation in GROMACS with GPU acceleration? As I currently understand to make use of GPU one need to use Ve

Re: [gmx-users] Free energy landscape by g_sham

On 2013-03-31 12:21, Kavyashree M wrote: Thank you Sir Note that the free energy differences are rigorously correct only if the array of the cells in the grid correspond units of phase space with the same volume. This is close to impossible to achieve, but the plots may still give insight.

Re: [gmx-users] Free energy landscape by g_sham

Thank you Sir Regards kavya On Sun, Mar 31, 2013 at 11:58 AM, bipin singh wrote: > g_sham calculates free energy landscapes by computing the joint > probability distribution from the two dimensional plane constructed > using two quantities (in your case it will be rmsd and radius of > gyration

Re: [gmx-users] Free energy landscape by g_sham

g_sham calculates free energy landscapes by computing the joint probability distribution from the two dimensional plane constructed using two quantities (in your case it will be rmsd and radius of gyration). Conformations sampled during the simulation were projected on this two dimensional plane, a

Re: [gmx-users] Free energy calculations with BAR and TI

--- On Fri, 2/11/12, Tom Kirchner wrote: > Actually, this is a known problem. You should find the > description and > solution in the archive. I had the same problem, so this may > make your > search more easy :) Thank you, it's good to know I'm not doing something wrong. Indeed, changing 298

Re: [gmx-users] Free energy calculations with BAR and TI

Hi Fernandez, Actually, this is a known problem. You should find the description and solution in the archive. I had the same problem, so this may make your search more easy :) The problem is in the code, at some point float and numbers are messed up, or something in this direction. You can

Re: [gmx-users] Free energy between residues

for GROMACS users > Betreff: Re: [gmx-users] Free energy between residues > > > On 6/28/12 6:51 AM, Steven Neumann wrote: > > On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul > wrote: > >> > >> > >> On 6/28/12 6:33 AM, Steven Neuma

Re: [gmx-users] Free energy between residues

On 6/28/12 6:51 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul wrote: On 6/28/12 6:33 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs wrote: Dear Steven, Where are you working? I work in UK, London. Why are you asking? >From

Re: [gmx-users] Free energy between residues

On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul wrote: > > > On 6/28/12 6:33 AM, Steven Neumann wrote: >> >> On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs wrote: >>> >>> Dear Steven, >>> >>> Where are you working? >> >> >> I work in UK, London. Why are you asking? >> >> >>> >From my experience

Re: [gmx-users] Free energy between residues

On 6/28/12 6:33 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs wrote: Dear Steven, Where are you working? I work in UK, London. Why are you asking? >From my experience the g_energy -fee only gives a free enrgy estimate for the whole system, so one has to pull

Re: [gmx-users] Free energy between residues

On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs wrote: > Dear Steven, > > Where are you working? I work in UK, London. Why are you asking? > >From my experience the g_energy  -fee only gives a free enrgy estimate for > >the whole system, so one has to pull out all the energy terms based on your

Re: [gmx-users] Free energy between residues

Dear Steven, Where are you working? >From my experience the g_energy -fee only gives a free enrgy estimate for the >whole system, so one has to pull out all the energy terms based on your index >file of interest and sum them in a spread sheet. if the -fee can do the >energy estimates for a s

Re: [gmx-users] Free energy calculation about ions (hope Justin A. Lemkul can give some suggestions )

On 5/9/12 10:37 PM, DeChang Li wrote: Dear all, I want to calculate the ion solvation free energy (e.g. an ion Na+ solvated in a water box) using Bennett Acceptance Ratio (BAR) method, following the tutorial by Justin A. Lemkul. However, if I turn off the Coulombic interaction, the tota

Re: [gmx-users] Free energy between surfaces

Cheers pal! :) Steven On Sat, Feb 18, 2012 at 9:42 AM, Jianguo Li wrote: > One way to get the free energy is to measure the force as a function of > distance and do the integration to get the PMF, as used in the paper: > Ronen Zangi, Morten Hagen, and B. J. Berne. 2007. Effect of Ions on the >

Re: [gmx-users] Free energy between surfaces

One way to get the free energy is to measure the force as a function of distance and do the integration to get the PMF, as used in the paper: Ronen Zangi, Morten Hagen, and B. J. Berne. 2007. Effect of Ions on the Hydrophobic Interaction betweenTwo Plates. J. AM. CHEM. SOC. 2007, 129, 4678-468

Re: [gmx-users] Free energy tutorial 6

murat özçelik wrote: hi! again.. ı collect all .xvg files into a single file.. and run g_bar You can't do that. g_bar requires multiple input files, as I stated before. -Justin g_bar -f md.xvg -o -oi -oh the program gave me below result hayalet@ubuntu:~/Masaüstü$ g_bar -f md.xvg -o -oi

Re: [gmx-users] free energy tutorial 6

murat özçelik wrote: hi all! ı am doing tutorial 6 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html ı have a problem.. ı am collect all md

Re: [gmx-users] Free Energy tutorial - choosing number of solvent molecules

Fabian Casteblanco wrote: Hello all, I'm running the same process from the free energy tutorial by Justin Lemkul...http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html. How did the number of solvent particles get chosen (in the tutorial, 210 molecul

Re: [gmx-users] free energy (coordinates file)

On 7/01/2012 9:12 PM, parto haghighi wrote: Dear GMX users, I have a question about 6th gromacs tutorial. That's not a useful description, because nobody else knows what list you're looking at. A URL is much better. I have to perform 5 steps of calculation contain: 1) EM-1 2) EM-2 3) NVT 4)

Re: [gmx-users] free energy and charges

parto haghighi wrote: Dear GMX users, when I want to correct charge group of one molecule I have to do calculate its free energy. I did this work by applying 6th gromacs tutorial. In this tutorial user has to assign 0 value in topology: [ atoms ] ; nr type resnr residue atom cgn

Re: [gmx-users] free energy and UB term

On 16/12/2011 7:22 AM, lq z wrote: Dear GMXers, I'm trying to manually add two sets of Urey-Bradley terms to the topology file (in [angle] entry with type 5). However, it seems it is not allowed. I got the following error: Incorrect number of parameters - found 8, expected 4 or 4 for U-B. I

Re: [gmx-users] free energy calculation " State B has non-zero total charge: 5.800000e+01 "

Chunxia Gao wrote: Dear gmx users: I am using the free energy to calculate the ligand binding affinity to protein, during the decouple process, I need to put some restraint between the protein and the ligand, e.g. distance restraint. But distance restraint is only for intramolecular, so I

RE: [gmx-users] Free Energy Question

I think using Perturbation method is more appropriate for this kind of free energy calculation. Check Leach, Molecular Modelling Principle and Applications pp 554-568. Its clearly described there and you can implement it in GROMACS. Cheers, Emanuel

Re: [gmx-users] Free energy sampling using G_bar

Fabian Casteblanco wrote: Hello all, I am finished running a free energy calculation using g_bar and i followed Justin Lemkuls tutorial and I am in the process of analyzing inorder to determine if I had adequate sampling. I have read the 'BAR' paper by Bennett but there are still some concern

Re: [gmx-users] Free energy calculation question

Fabian Casteblanco wrote: Hello Justin, I'm calculating the free energy of a drug in an alcohol solvent. I have a question referring to your free energy tutorial. You mentioned that decoupling of electrostatic interactions is linear and decoupling of vdW can vary. Is this true for your case

Re: [gmx-users] Free Energy Integrator Selection

Hi there, I am also doing FEP calculations and I am also using sd as integrator. The problem that I am having with this integrator is the temperature coupling (NTP). I am setting the targeted temperature of the system on 300K, for 2 Groups, Protein_and_ligand and Solvent. g_energy gives me 303

Re: [gmx-users] Free Energy Integrator Selection

Fabian Casteblanco wrote: Dear all, I was running free energy calculation for a drug molecule in solvent. First, For [coulomb + vdW] --> [vdW] , I used 'md' integrator For [vdW] --> [none], I was using 'md' but it required me to switch to 'sd' based on this error message: "WARNING: For

Re: [gmx-users] Free energy calculation

Fabian Casteblanco wrote: Hello all, I am setting up a free energy calculation (drug from full coulomb+vdW in solution --> drug with only vdW in solution --> dummy drug in solution). After reading most of the papers, I understand that you need significant overlap from the energies for each in

Re: [gmx-users] free energy

Please see this... http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html Raghu On Sun, Jul 10, 2011 at 12:33 PM, balaji nagarajan wrote: > Dear Users ! > > Is it possible to calculate the free energy for a molecule , > > at the zero step MD , when i see t

Re: [gmx-users] free energy calculations

Ragothaman Yennamalli wrote: Hi, I want to run free energy calculations on a particular protein-ligand complex. I do not have much knowledge on this so I have some questions, hopefully someone might give me clear answers. I am following the tutorial given in this link: http://www.bevanlab.bi

Re: [gmx-users] free energy

The current simulations are currently in vacuum. Does the following mdp file seem ok. Note that this is a production run using the final configuration after a lengthy equilibration. Also I was thinking about trying to prevent the other chains from entering the specific site; is there a a way to imp

Re: [gmx-users] free energy

Hi Chris My windows are restrained obviously using the force constant in the mdp file. The trajectories that I have viewed are those of the individual biased sampling windows. I have not put on the unbiased simulations yet. There is also the following issue: The simulations involve two identical m

Re: [gmx-users] free energy blank dgdl

hi It seems that your couple-moltype is missing, that is, no molecules will be turned off interaction. dawei On Thu, Feb 17, 2011 at 8:26 AM, Moeed wrote: > Hello Justin > > Thanks for your attention. Just to remind you: I am getting blank dgdl and > I found this in log file: > > > There are

Re: [gmx-users] free energy blank dgdl

Moeed wrote: Hello Justin Thanks for your attention. Just to remind you: I am getting blank dgdl and I found this in log file: > There are 0 atoms and 0 charges for free energy perturbation EM > > grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o e

Re: [gmx-users] free energy

One other thing I would point out is that the solvation free energy is dependent on concentration. you will get a different result with 4 polymer chains vs 3 vs 3, etc. Make sure you understand the dependence. Also, the free energy will depend on the polymer chain length. Polymer and finite con

Re: [gmx-users] free energy

  On February 14, 2011 at 3:28 PM Moeed wrote: Dear experts, I am going to do solvation FE of polymer (polyethylene) in a hydrocarbon solvent. I have prepared a system consisting of 4 polymer chains and 480 hexane

Re: [gmx-users] free energy

How close are the polymers in space? On February 14, 2011 at 3:28 PM Moeed wrote: Dear experts, I am going to do solvation FE of polymer (polyethylene) in a hydrocarbon solvent. I have prepared a system consistin

Re: [gmx-users] Free energy

The biotin-streptavidin interaction is on the order of -75 kJ/mol, so a binding free energy of -300 kJ/mol (dissociation constant of 10^-52 M) means something is fundamentally wrong - start by taking a hard look at your protocol, as convergence problems wouldn't account for that kind of deviatio

Re: [gmx-users] Free energy

mohsen ramezanpour wrote: Dear All I estimated protein-ligand free energy about -300 kj Is it logical?I think it is wrong.what do you think? There is no way for anyone on this list to assess such things. It sounds unphysical to me, but that's just a gut reaction based on nothing in particu

Re: [gmx-users] free energy of methan disappearing:tutorial

Dear Mustard Thanks very much for your useful notes and your reply Mohsen On Tue, Dec 28, 2010 at 7:48 PM, TJ Mustard wrote: > Yeah there is so much to do. > > 1. Build a methane in a program that allows saving of pdb. Make sure the > pdb and all the atoms are correctly formated. Or find a meth

Re: [gmx-users] free energy of methan disappearing:tutorial

Yeah there is so much to do. 1. Build a methane in a program that allows saving of pdb. Make sure the pdb and all the atoms are correctly formated. Or find a methane pdb or gro file. I think there is one off of Dr. Mobely's website.   2. yes (you don't even need a state

Re: [gmx-users] Free Energy Calculation: dVpot/dlambda is always zero

Anirban Ghosh wrote: Hello Justin, Thanks a lot for the reply. Yes, I am using GROAMCS 4.5 and my system consists of two chains of two proteins, a substrate and an inhibitor solvated in water. So can you please tell me what should be the values for: couple-moltype The name of

Re: [gmx-users] Free Energy Calculation: dVpot/dlambda is always zero

Hello Justin, Thanks a lot for the reply. Yes, I am using GROAMCS 4.5 and my system consists of two chains of two proteins, a substrate and an inhibitor solvated in water. So can you please tell me what should be the values for: couple-moltypecouple-lambda0couple-intramolThanks a lot again. Rega

Re: [gmx-users] Free Energy Calculation: dVpot/dlambda is always zero

Anirban Ghosh wrote: Hi ALL, I am trying to run free energy calculation and for that in the md.mdp file I am keeping the following option: ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda= 0 sc_alpha=0.5 sc-power=1.0 sc-sigma=

Re: [gmx-users] free energy perturbation

antonio wrote: Dear gromacs users I am trying to carry out a free energy perturbation to evaluate the difference in binding energy between two inhibitors of the same protein. I have read a lot of post but i did no understand how to create the topology file. have i to write a mixed pdb of the tw

Re: [gmx-users] Free energy calculations - desolvation energy of Na+

eva.pluhar...@marge.uochb.cas.cz wrote: Hi Justin, thank you for suggestion about changing the integrator, but I would like to know why it is not possible to sample properly by md under these circumstances. 1. Do you know any papers about sampling efficiency of systems with almost or complete

Re: [gmx-users] Free energy calculations - desolvation energy of Na+

eva.pluhar...@marge.uochb.cas.cz wrote: Hello all, I am trying calculate desolvation free energy of Na+ in water using option couple-moltype, not by creating B-topology in the .top file. At first, I switched off coulombic interaction using: couple-moltype = Na+ couple-lambda0

Re: [gmx-users] free energy decomposition[David Van der Spoel]

Sent: Wed, October 13, 2010 1:42:41 PM Subject: Re: [gmx-users] free energy decomposition On 10/13/10 8:30 PM, Chris Neale wrote: > Sanku, > > This is not possible using g_energy or any other gromacs tool that I am aware >of. > You must calculate the temperature derivative of

Re: [gmx-users] free energy decomposition

Chris, I am aware of that paper by Pettit and Rossky where the suggested method is to get the entropy first by taking temperature derivative and substract that from PMF to get the enthalpy contribution . BUT, also if you look at the recent paper by Berk Hess , J.Phys.chem B , 2010;114:11093

Re: [gmx-users] free energy decomposition

On 10/13/10 8:30 PM, Chris Neale wrote: Sanku, This is not possible using g_energy or any other gromacs tool that I am aware of. You must calculate the temperature derivative of the free energy. See, for example, equation 16 in Pettitt BM, Rossky PJ. J Chem Phys. 1986;84:5836 Recent versions

Re: [gmx-users] free energy calculation problem

Павел Кудрявцев wrote: Hi, I wanna perform free energy calculation by changing parameters of amino acid residue. Since my case is rathe complicated first I tried to perform a very simplified task - to change only charges of atoms. So I peeked out one residue, keeped all its atom types and mass

Re: Re: [gmx-users] Free Energy Calculation

>> Hello, dear users! >> >> I want to study different components in total free energy. >> Could you tell me in what gromacs program and in what place exactly force and energy are calculated? >I think your question is too general. I don't know whether you've already done a calculation, are planning

Re: [gmx-users] Free Energy Calculation

- Original Message - From: Петр Попов Date: Thursday, September 30, 2010 22:39 Subject: [gmx-users] Free Energy Calculation To: gmx-users@gromacs.org > Hello, dear users! > > I want to study different components in total free energy. > Could you tell me in what gromacs program and in w

Re: [gmx-users] Free Energy calculations of peptide-protein binding

Hi Ehud, we recently developed an extended amber99sb forcefield + some scripts which probably can do exactly what you want (setting up alchemical mutations for any amino acid mutation except for proline). We tested it by calculating thermostability differences for a set of 100+ mutations of an

Re: [gmx-users] free energy landscape question

Dear Antonio, thank you. I think I got the idea. I need to use a cut-off for the probability: for all the probabilities lower than a certain value I assign to them that (lower) value so the energy will be constant. Thanks, Andrei On Wed, Jun 23, 2010 at 8:49 PM, wrote: > > On Wed, 23 Jun 2010,

Re: [gmx-users] free energy landscape question

On Wed, 23 Jun 2010, Andrei Neamtu wrote: Dear Andreas and Marc, Thanks for your reply. I am not familiar with the gromacs programming code and so I am trying to build myself the FEL. I can generate the hisotgram of the number of states from the projection along principal component 1 and 2 (PC1

Re: [gmx-users] free energy landscape question

Dear Andreas and Marc, Thanks for your reply. I am not familiar with the gromacs programming code and so I am trying to build myself the FEL. I can generate the hisotgram of the number of states from the projection along principal component 1 and 2 (PC1 and PC2) using SigmaPlot but here I am stucke

Re: [gmx-users] free energy landscape question

On Wed, Jun 23, 2010 at 10:20:19AM +0100, Kukol, Andreas wrote: > Yes, that is an interesting question. I don't know the answer, but is there > any way to get the numerical values of the matrix from Gromacs tools that > produce a matrix in xpm format ? I have problems with g_rms and g_rmsdist is

RE: [gmx-users] free energy landscape question

Yes, that is an interesting question. I don't know the answer, but is there any way to get the numerical values of the matrix from Gromacs tools that produce a matrix in xpm format ? I have problems with g_rms and g_rmsdist is another candidate. Andreas > -Original Message- > From: gmx

Re: [gmx-users] Free Energy Calculation

Hi Anirban, You *could* use the configurations in your trajectory to (re)calculate average energies; by de-coupling your ligand this would get you the average free energy change per coupling strength change at the point where the ligand is fully bound. If you're interested in free energy of bi

Re: [gmx-users] free energy

afsaneh maleki wrote: Hi, I inserted the protein in bilayer at Z normal and simulated membrane protein. to calculate free energy, it is better to use "umbrella sampling tutorial " from Justin Lemkul or "free energy tutorial" from David Mobley for my system? That depends entirely upon t

Re: [gmx-users] free energy

On 1/10/10 7:53 PM, Nilesh Dhumal wrote: Justin, Here I have pasted the data about free energy from mdout.mdp file ; Free energy control stuff free_energy = yes init_lambda = 0.20 delta-lambda = 0 sc-alpha = 0.6 sc_power = 1

Re: [gmx-users] free energy

Justin, Here I have pasted the data about free energy from mdout.mdp file ; Free energy control stuff free_energy = yes init_lambda = 0.20 delta-lambda = 0 sc-alpha = 0.6 sc_power = 1 sc-sigma = 0.3 couple-moltyp

Re: [gmx-users] free energy

On 1/10/10 7:02 PM, Nilesh Dhumal wrote: Thanks Justin, I am not setting any Lennard-Jones parameters to zero for part B. I put zero charge on all atoms for Part B. (Lennard Jones parameters for B are same as Part A). Under Gromacs 4.0.x, you should be able to leave the topology alone entire

Re: [gmx-users] free energy

Thanks Justin, I am not setting any Lennard-Jones parameters to zero for part B. I put zero charge on all atoms for Part B. (Lennard Jones parameters for B are same as Part A). I am using default parameters for "couple-lambda0" and "couple-lambda1". For one of my simulation (glucose + ionic liq

Re: [gmx-users] free energy

On 1/10/10 1:03 PM, Nilesh Dhumal wrote: Hello Justin, Should I add dum_opls no. in atom type file in which Lennard-jones parameters will set to zero. OR. I don't have to modify anything prog.will take care of lennard-jones interactions. I have put charge zero on all atom in TYPE B. You shou

Re: [gmx-users] free energy

Hello Justin, Should I add dum_opls no. in atom type file in which Lennard-jones parameters will set to zero. OR. I don't have to modify anything prog.will take care of lennard-jones interactions. I have put charge zero on all atom in TYPE B. Nilesh On Sun, January 3, 2010 12:57 pm, Justin A. Lem

Re: [gmx-users] free energy

Nilesh Dhumal wrote: THanks Justin. I am using Groamcs 4.0.7 version. I will do more simulation with more lambada value betwen 0 to 0.1. I really think this is less significant than point #1 I mentioned before. Be sure you are actually setting the relevant .mdp parameters (couple-lambda0,

Re: [gmx-users] free energy

THanks Justin. I am using Groamcs 4.0.7 version. I will do more simulation with more lambada value betwen 0 to 0.1. Thanks. Nilesh On Sun, January 3, 2010 12:39 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hey All, >> I am trying to calculate the solvation free energy of glucose in

Re: [gmx-users] free energy

Nilesh Dhumal wrote: Hey All, I am trying to calculate the solvation free energy of glucose in ionic liquids. I am getting really large value for lamda=0 in vacuum and solvent as well. I am getting final solvation energy value ~ 310 kJ/mol. Can you tell me where I am wrong. There are sever

Re: [gmx-users] free energy perturbation

I will try the second solution you proposed (which seems more flexible). So, I should edit the top file (as explained in the "Topologies/File formats/Topologies for free energy calculations" section of the manual). And I should NOT use "couple-moltype" anymore, which is just a shortcut for the sta

RE: [gmx-users] free energy perturbation

> From: giovanni.bu...@gmail.com > Date: Mon, 14 Dec 2009 13:47:37 +0100 > To: gmx-users@gromacs.org > Subject: [gmx-users] free energy perturbation > > Dear all, > > I am using GROMACS with free-energy perturbation to switch off a > molecule gradually. If I understand correctly, the parameter

Re: [gmx-users] free energy calculations using MBAR and gromacs

This looks like more of a pymbar question! >  I am trying to calculate free energy of a system that involves > disappearance of LJ particle at lambda=1 in explicit solvent. I ran the > simulation at 20 different lambda points ranging from 0 to 1, using soft > core potential. In order to use MBAR m

Re: [gmx-users] Free energy calculations

Can you be more specific in the question of what property you want to compute for which molecule or molecules? Linear Interaction energy approaches are not always very efficient for coulomb, and is definitely not exact for the LJ term. So LIE might not be what you want to be doing. Michael Shirts

Re: [gmx-users] Free Energy

b95203...@ntu.edu.tw wrote: Hi all, I have some pdb file of peptides that I wish to do free energy calcuation. Is there any source I can do that? http://www.gromacs.org/Documentation/How-tos/Free_Energy_Calculations If you want a more specific answer, ask a more specific question. -Justin

RE: [gmx-users] free energy problem

Hi, You seem to be trying to decouple a 9 residue peptide from the rest of the system. This "brute-force" approach will only work when you have an enormous amount of computer power and you will have to tune all your parameters carefully. You should consider if this approach is feasible. You cra

RE: [gmx-users] free energy coupling/decoupling equivalence

Hi, If you are talking about equilibrium methods, for instance free energy intergration or Bennett's acceptance ratio, there is no directionality. You might start a simulations at a lamba point with the end configuration of the previous lambda, which could introduce some directionality, but the

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Thank you David I would certainly try this way. On Mon, Feb 9, 2009 at 1:08 PM, David Mobley wrote: > Hi, > >> Thanks David, But if I just remove the Copper atom and do the >> simulation as copper is charged there would be sudden change in >> electrostatics and the protein started unfolding when

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Hi, > Thanks David, But if I just remove the Copper atom and do the > simulation as copper is charged there would be sudden change in > electrostatics and the protein started unfolding when I ran the > simulation for 10ns. So I thought perturbing the charge by little > every time I can get a struc

Re: [gmx-users] Free energy perturbation of Cu(I) binding

abhigna polavarapu wrote: Hey Mark, I am just not getting the theory behind doing position restraints and applying them to equilibrate. Sure... so that's why I recommended chapter 5 (which has an example of position restraints in section 5.7.1, which you can understand with references to the

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Hey Mark, I am just not getting the theory behind doing position restraints and applying them to equilibrate. So let me frame my question well. Cu(I) is binding to three amino acids in the protein. Now If I remove Cu(I) the -1 charge of the protein changes to 0. So the protein has two specific cha

Re: [gmx-users] Free energy perturbation of Cu(I) binding

abhigna polavarapu wrote: Thanks Mark, thats what I really wanted to do. So can you please let me know where I can find out the way to do position restraints and to know how these work. Chapter 5 in the manual, or some tutorial material (perhaps from the wiki). Mark ___

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Thanks Mark, thats what I really wanted to do. So can you please let me know where I can find out the way to do position restraints and to know how these work. abhigna On Tue, Feb 3, 2009 at 10:18 PM, Mark Abraham wrote: > abhigna polavarapu wrote: >> >> Thanks David, But if I just remove the Co

Re: [gmx-users] Free energy perturbation of Cu(I) binding

abhigna polavarapu wrote: Thanks David, But if I just remove the Copper atom and do the simulation as copper is charged there would be sudden change in electrostatics and the protein started unfolding when I ran the simulation for 10ns. So I thought perturbing the charge by little every time I ca

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Thanks David, But if I just remove the Copper atom and do the simulation as copper is charged there would be sudden change in electrostatics and the protein started unfolding when I ran the simulation for 10ns. So I thought perturbing the charge by little every time I can get a structure with more

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Perhaps this is obvious, but typically you only want to do free energy perturbation if you are interested in computing a free energy difference. If you are merely interested in structural properties of a different system (in this case, the protein without the copper there) you can simply make the c

RE: [gmx-users] free energy with TIP4P bug fixed

dear Berk, please let us know whether following patch is correct for 3.3.1 diff orig-ns.c ns.c 2c2 < * $Id: ns.c,v 1.84.2.3 2006/03/01 07:57:46 spoel Exp $ --- * $Id: ns.c,v 1.84.2.3.1 2009/02/03 20:27:00 hess Exp $ 617c617 < bool bDoVdW_i,bDoCoul_i; --- bool bDoVdW_i,bDoCo

RE: [gmx-users] free energy with TIP4P bug fixed

Hi, There are three ways to avoid this bug with free-energy and TIP4P: Or make sure that any energy group that contains perturbed atoms does not include any non-perturbed atoms with charges, or use GMX_NO_SOLV_OPT (slow), or use the fix below. Berk RCS file: /home/gmx/cvs/gmx/src/mdlib/ns.c,v r

RE: [gmx-users] free energy decomposition

Hi, Currently you can only get a decomposition every nstlog steps in the log file with the mdrun option -seppot. However, only the sum of VdW and Coulomb will be reported. Berk > Date: Tue, 3 Feb 2009 16:16:55 +0800 > From: friendli2...@gmail.com > To: gmx-users@gromacs.org > Subject: [gmx-user

RE: [gmx-users] free energy with TIP4P bug fixed

Hi, Sorry for not being clear on this issue. I am currently following and preparing lectures and exercises for a workshop and do not have time to sit back and go deeply into this issue. What my conclusion is from looking at the code: With TIP4P water and free-energy any non-perturbed atoms that

Re: [gmx-users] free energy with TIP4P bug fixed

Yes, I could use clarification here as well. I had previously suspected a specific bug relating to the free energy code and water models (TIP4P-Ew) and contacted the list about this a few weeks ago. At that time Berk told me that there was no water-specific free energy code, which I take to mean t

Re: [gmx-users] Free energy of transfer with accuracy

ater structure generally are well known and studied. David > Thank you > eef > ___ > Eudes Eterno Fileti > Centro de Ciências Naturais e Humanas > Universidade Federal do ABC > Rua Santa Adélia, 166 - Bloco B, Sala 1048 > 09210-170 Santo André - SP Brasil > +55.11.4437

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