[gmx-users] free energy

Dear Kieu Thu  Thanks for your comment about free energy. Unfortunately, I could not send a email to Paissoni Cristina in the Gromacs Forum.  Could you give me email address of Paissoni Cristina? Finding a tool for calculation MM/PBSA with Gromacs is very vital for me.  Best Regards  Kiana --

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

[gmx-users] free energy

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 consideration. Best Regards Kiana  -- gmx-user

[gmx-users] Free energy of solvation of large molecule

Hi, I'm trying to calculate the free energy of solvation of a relatively large polymer molecule (161 atoms). I went through the free energy tutorial published on J. Lemkul's web page but when trying to apply the same approach to my case, the simulations typically fail. The files for one such case

[gmx-users] Free Energy Ion Pair Decoupling

Dear Gromacs users, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interf

Re: Aw: [gmx-users] Free Energy Simulations in Parallel

tin Sincerely, Stephan Watkins *Gesendet:* Freitag, 26. Juli 2013 um 22:13 Uhr *Von:* "Quintin Sheridan" *An:* "gmx-users@gromacs.org" *Betreff:* [gmx-users] Free Energy Simulations in Parallel Dear Gromacs Users, Is it possible to run free energy calculations in parallel using

Aw: [gmx-users] Free Energy Simulations in Parallel

n Sheridan" An: "gmx-users@gromacs.org" Betreff: [gmx-users] Free Energy Simulations in Parallel Dear Gromacs Users, Is it possible to run free energy calculations in parallel using mpirun? If not, what is the fastest way to run free energy calculations. I am trying to us the B

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

[gmx-users] Free Energy Simulations in Parallel

Dear Gromacs Users, Is it possible to run free energy calculations in parallel using mpirun? If not, what is the fastest way to run free energy calculations. I am trying to us the Bennet's Accepetance Ratio (g_bar) to get the free energy of solvation for an ionic liquid based on the tutorial by

[gmx-users] Free Energy Calculations in Parallel

Dear Gromacs Users, Is it possible to run free energy calculations in parallel using mpirun? If not I am wondering what the fastest way to run a free energy calculation is. I am basing my free energy calculation on the tutorial by Justin Lemkul found at http://www.bevanlab.biochem.vt.edu/Pages/Pe

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

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

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 installed in two identical Linux boxes. Howe

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

> *Gesendet:* Donnerstag, 30. Mai 2013 um 20:48 Uhr > *Von:* "Dejun Lin" > *An:* gmx-users@gromacs.org > *Betreff:* [gmx-users] Free energy calculation: merge the topology of 2 > molecules > Hi all, > > I'm trying to set-up a free energy calculation where a

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

tions though.   Stephan   Gesendet: Donnerstag, 30. Mai 2013 um 20:48 Uhr Von: "Dejun Lin" An: gmx-users@gromacs.org Betreff: [gmx-users] Free energy calculation: merge the topology of 2 molecules Hi all, I'm trying to set-up a free energy calculation where a molecule has +2 charge

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

Hi all, I'm trying to set-up a free energy calculation where a molecule has +2 charge in it's native state (state A) and no charge in the mutant (state B). Since the molecule has net +2 charge, I have to add counter-ions to neutralize the system in state A. But in order to transform it to state B

[gmx-users] Free energy of solvation's .mdp of peptide

Hi, if I want to calculate the free energy of solvation of peptide, because both van der Waals and Coulombic interactions are important for peptide so I set couple-lambda0 = none couple-lambda1 = vdw-q is it right? or it's better to choose wo-stage approach to do this work: van der

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

[gmx-users] free energy of system

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? (The calculated total energy and entha

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

[gmx-users] Free Energy Calculations in Gromacs

Hi, I am trying to perform expanded ensemble simulations between 2 states A (lambda=0) and B (lambda =1) with 6 intermediate lambda values. In state B the Hamiltonian is rescaled, such that the epsilons of the vdW interactions, the charges, the bond, angle and dihedral constants are a multiple of

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

[gmx-users] Free energy on GPU?

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 Verlet cutoff scheme. When I do so with pme

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

[gmx-users] Free energy landscape by g_sham

Dear users, Can someone kindly explain how g_sham calculates the free energy landscape of given two quantities say, rmsd and radius of gyration. Any references are welcome. Thank you with Regards Kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/

[gmx-users] free energy

Dea GROMACS Users, I want to calculate the free energy for my system, for example (Gibbs and Helmholtz), but I didn't define the free_energy in the md.mdp and my simulation has been finished!!! May I ask you that say me is there a solution fro this problem? Best Regards Sara -- gmx-users mai

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

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

Hi all, Can I use the same simulations (with delta_lambda=0, init_lambda and foreign_lambda) for TI and BAR calculations? I guess that boils down to whether the simulations with foreign_lambda are in equilibrium with the init_lambda, or they are some sort of hybrid ensemble between the differen

[gmx-users] Free energy calculation on a frozen fragment

Hi all, I'm interested in calculating the free-energy change when a frozen part of the system changes. The change, in general, implies a change in coordinates and in non-bonded parameters. As far as I know, there's no efficient way to calculate this currently in gromacs. The only way I see is

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

ulombic) and then can get the effective potential Ueff=-kTln Sincerely, > > Stephan Watkins > > Original-Nachricht >> Datum: Thu, 28 Jun 2012 09:28:09 +0100 >> Von: Steven Neumann >> An: Discussion list for GROMACS users >> Betreff: [gmx-users] F

Re: [gmx-users] Free energy between residues

imates for a specific set, please let me know this would be valuable >to me. Sincerely, Stephan Watkins Original-Nachricht > Datum: Thu, 28 Jun 2012 09:28:09 +0100 > Von: Steven Neumann > An: Discussion list for GROMACS users > Betreff: [gmx-users] Free energy b

[gmx-users] Free energy between residues

Dear Gmx Users, I want to obtain the free energy difference between the pair of residues in my protein chain with respect to thheir distance. Would combinbation: 1) g_dist - distances between two groups during the simulation time 2) g_energy -fee (DelatG - with energy groups I am interested in 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

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

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 total charge of my system would not neutral at

[gmx-users] Free Energy calcualtions

Hi Gromacs Users, I want to mutate a glutamate in my protein to alanine in presence of a ligand. With glutamate, the protein charge is -3. To neutralize the system, I added 3K+ ions. Now when I mutate GLU to ALA, the charge in state_B will be +1 (protein -2 + 3K+). Right now I'm in the charge part

[gmx-users] free energy calculation and g_bar error

Dear gmx-users: I was trying to do a free energy calculation of a charged ligand, according to the paper "Calculation of Absolute Binding Free Energies for Charged Ligands and Effects of Long-Range Electrostatic Interactions ", one of the problems with charged ligands is that the use of a sol

Re: [gmx-users] Free energy between surfaces

ns on the > Hydrophobic Interaction between Two Plates. J. AM. CHEM. SOC. 2007, 129, > 4678-4686 > > Jianguo > -- > *From:* Steven Neumann > *To:* Discussion list for GROMACS users > *Sent:* Saturday, 18 February 2012, 17:25 > *Subject:* [gmx

Re: [gmx-users] Free energy between surfaces

-4686 Jianguo From: Steven Neumann To: Discussion list for GROMACS users Sent: Saturday, 18 February 2012, 17:25 Subject: [gmx-users] Free energy between surfaces Dear Gmx Users, I am wondering whether you know a technique for calculating the free energy

[gmx-users] Free energy between surfaces

Dear Gmx Users, I am wondering whether you know a technique for calculating the free energy between charged surfaces - I want to calculate distance when the deltaG=0 so that the surfaces are in equilibrium - closer distance will make that they repeal each other, longer (deltaG<0). Will Umbrella Sa

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

[gmx-users] Free energy tutorial 6

hi! again.. ı collect all .xvg files into a single file.. and run g_bar g_bar -f md.xvg -o -oi -oh the program gave me below result hayalet@ubuntu:~/Masaüstü$ g_bar -f md.xvg -o -oi -oh :-) G R O M A C S (-: Good ROcking Metal Altar for Chronic

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

[gmx-users] free energy tutorial 6

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.xvg files and run g_bar with below command.. g_bar -f md.xvg -o -oi -oh.. the program gave me the following error.. Why do

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

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

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 molecules were chosen)? I seem to be

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)

[gmx-users] free energy (coordinates file)

Dear GMX users, I have a question about 6th gromacs tutorial. I have to perform 5 steps of calculation contain: 1) EM-1 2) EM-2 3) NVT 4) NPT 5) Product MD for each Lambda value from 0 up to 1. I have a .gro file contains initial coordinates of my system : drg.gro For lambda = 0.00 I have done 5 st

[gmx-users] Free Energy of a mutated molecule

Hello all, Please if anybody can help. I'm trying to mutate a -CH3 to an -H (I guess with 3 dummy atoms attached to it). Below I sketched the process. I broke it up into 3 steps and I wanted to use g_bar for the actual mutation step (step 2). Does anybody have any experience with something

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

[gmx-users] free energy and charges

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 cgnr charge mass type

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

[gmx-users] free energy and UB term

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. Is it true that I can't do this in gromac

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

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

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 need to make a hybrid

RE: [gmx-users] Free Energy Question

- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Fabian Casteblanco Sent: Tuesday, 4 October 2011 6:28 AM To: gmx-users@gromacs.org Subject: [gmx-users] Free Energy Question Hello all, I have a general question about calculating free energies. I recently

[gmx-users] Free Energy Question

Hello all, I have a general question about calculating free energies. I recently used g_bar to calculate the free energies of decoupling coulombic and vdW forces of a solute molecule in solvent. I now need to calculate the free energy of a solute molecule mutating to a new molecule (identical bu

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

[gmx-users] Free energy sampling using G_bar

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 concerns whether I have enough sampli

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

[gmx-users] Free energy calculation question

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 of methanol in water or for a

[gmx-users] Free energy

g_lie calculates the deltaG= alpha(p - w) + beta(p - w) equation. But when calculating DGbind from g_lie it will ask for only one term at a time i.e. -Elj for either p or w and -Cqq for either p or w. My question is when using only p for -Elj and Vl-s el>p for -Cqq, how the LJ and EL terms calcul

[gmx-users] Free Energy Integrator Selection

Try running for longer and look at the convergence of the temperatures over time. I suspect that what you are reporting is actually just statistical noise. I am not sure about using the sd integrator and defining multiple temperature coupling groups... If you define the same temperature for

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

[gmx-users] Free Energy Integrator Selection

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 proper sampling of the (nearly

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

[gmx-users] Free energy calculation

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 intermediate point to overlap so

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

[gmx-users] free energy

Dear Users ! Is it possible to calculate the free energy for a molecule , at the zero step MD , when i see the mail list this question has been posted once , but i could not find the reply for this ! is there any option for this like g_energy !

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

[gmx-users] free energy calculations

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.biochem.vt.edu/Pages/Personal/justin/g

[gmx-users] free energy

Dear Gavin: I'm not seeing a lot of effort on your part to answer these questions. I suspect that you can answer some of this. Good luck! Chris. -- original message -- The current simulations are currently in vacuum. Does the following mdp file seem ok. Note that this is a production run us

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

[gmx-users] free energy

yes it will, and so will it affect the profile if water molecules or ions go in when both chains are absent. You'll need to determine what question you are trying to answer and also think pretty hard about what your PMF really means in the context of this system. Chris. -- original messa

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

[gmx-users] free energy

Your windows are restrained. The PMF that you get out of WHAM is a representation of the relative sampling after removing the umbrella biases. Sounds like you are saying that you look at the still-biased trajectories and you see different a different distribution of states than you do in th

[gmx-users] free energy

Hi all I have performed a PMF simulation of taking part of a molecule out of the cavity of a host using umbrella sampling. The free energy curve suggests that the guest prefers to be outside the host as the bound state is higher in energy, or the free energy difference to go in is positive. Howeve

[gmx-users] free energy perturbation

Hello, I am doing free energy perturbation for ethane to methanol conversion. Can anybody tell me which of the following way is right to define virtual site for hydrogen? [ virtual_sites2 ] 3 2 1 1 0.00 or [ virtual_sites2 ] 3 2 1 1 1.00 Thanking you in anticipation. With regards, Jignesh

[gmx-users] Free energy calculation and position restraint

Dear all >From Table 5.6 of Gromacs 4.5.4 manu, position restrain constants can be interpolated in free energy calculations. However, I cannot find how to set up this. Can somebody help? thanks. dawei -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

[gmx-users] free energy-couple-intramol options

Hello, I read through the couple-intramol options (yes and no) good many times but I can not still realize what is the difference and which option I should select. I am having a hydrocarbon system (polyethylene in hexane as solvent). Can anyone help me understand these options please? (in plain en

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

[gmx-users] free energy blank dgdl

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 em-l0.tpr >& > output.g

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

[gmx-users] free energy

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 molecules with the actual density of polymer solution (~ 0.5 g/cm3). 1- For such a study I dont know how many polymers I need to h

[gmx-users] free energy calculation , grompp crash

Dear users I tried free energy calculation but grompp couldn't go through. It stops after *** Generated 2278 of the 2278 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2278 of the 2278 1-4 parameter combinations Excluding 3 bonded neighbours m

Re: [gmx-users] Free energy

nd of deviation. From: mohsen ramezanpour To: Discussion list for GROMACS users Sent: Wed, 29 December, 2010 20:36:59 Subject: [gmx-users] Free energy Dear All I estimated protein-ligand free energy about -300 kj Is it logical?I think it is wrong.what do you think? wh

[gmx-users] Free energy

In addition to Justin's comments, check your convergence with block averaging. Is there a systematic energy drift as you increase the amount of sampling prior to each block? Also, try applying your method to Na+ and Cl- in a box of water. If you can't get that free energy correctly, then yo

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

[gmx-users] Free energy

Dear All I estimated protein-ligand free energy about -300 kj Is it logical?I think it is wrong.what do you think? what is the range of correct value for a typical protein-ligand? protein=660 residue ligand=25 atom water=4670 Na=118 Cl=120 thanks in advance -- gmx-users mailing listgmx-users

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