Re: [gmx-users] FEP

Hi Fabian, I am trying something similar with Glutamate to Alanine mutation. Does your dummy atoms i.e., DUM1 have a value of 0.0 for sigma and epsilon during all three steps or only in step 2? Thanks for the time, Sai On Thu, Apr 26, 2012 at 10:43 AM, Fabian Casteblanco < fabian.castebla...@gma

Re: [gmx-users] FEP for ligand mutation

On 23/01/2012 7:06 AM, Sanku M wrote: Hi, Is it possible in GROMACS4.5 to perform computation of relative binding free energy of a ligand to a protein due to mutation in the ligand ( or due tio mutation in the protein)? I have done the computation of solvation free energy of a solute in a so

Re: [gmx-users] FEP

> So BAR is only > referring to the mathematical code used to calculate the overall free > energy for the FEP, correct? Yes. The information required is the same, with the exception that exponential averaging requires energy differences from only one state, whereas BAR requires energy differences

Re: [gmx-users] FEP

FEP is a poorly defined term. It can either mean 1) making small changes 'alchemical' changes in the molecules and computing the free energies by any method (BAR, TI, etc), or 2) it can mean specifically computing the free energies by exponentially averaging the potential energy differences. Basi

Re: [gmx-users] FEP

Steven Neumann wrote: Thank you guys! So, is there any tutorial in Gromacs for calculating free energy of ligand binding using FEP? TI or BAR are better methods for calculating binding free energies, I would think. FEP is best for mutating between different species. -Justin Steven On

Re: [gmx-users] FEP

Thank you guys! So, is there any tutorial in Gromacs for calculating free energy of ligand binding using FEP? Steven On Mon, Oct 10, 2011 at 2:02 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Hi >> Please have a look at Dr.Justin tutorial page at the following link: >> >> htt

Re: [gmx-users] FEP

mohsen ramezanpour wrote: Hi Please have a look at Dr.Justin tutorial page at the following link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html This tutorial is not for FEP explicitly, but may be of some use. There is discussion on using the BAR algorit

Re: [gmx-users] FEP

Hi Please have a look at Dr.Justin tutorial page at the following link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html Cheers On Mon, Oct 10, 2011 at 12:27 PM, Steven Neumann wrote: > Hi Gmx Users, > > Can you suggest some reading and some tutorial in calculat

Re: [gmx-users] FEP charged molecule cuestion

This is a tough issue and there are some unresolved questions here. I recommend seeing the work of Kastenholz and Hunenberger on ion solvation in JCP a couple years ago (two companion papers) as these explain the key issues. Thanks. On Wed, Aug 17, 2011 at 3:24 AM, Marcelino Arciniega Castro < m

Re: [gmx-users] FEP and loss of performance

Ok. I agree with you, FEP performance is an important issue to resolve but I know that there are also other priorities. However, I would thank you for your interest and and your suggestions. Luca > I would suggest that you take Chris' advice and post all of this as a > feature request on redmi

Re: [gmx-users] FEP and loss of performance

I would suggest that you take Chris' advice and post all of this as a feature request on redmine.gromacs.org so that it can be put on a to-do list. Enhancing the performance of the free energy code is probably going to be a low-priority, long-term goal (in the absence of any proven bug), but

Re: [gmx-users] FEP and loss of performance

I posted my test files in: https://www.dropbox.com/link/17.-sUcJyMeEL?k=0f3b6fa098389405e7e15c886dcc83c1 This is a run for a dialanine peptide in a water box. The cell side cubic box was 40 A. The directory is organized as : TEST\ topol.top Run-00/confout.gro; Equilibrated stru

Re: [gmx-users] FEP and loss of performance

David Mobley wrote: Hi, This doesn't sound like normal behavior. In fact, this is not what I typically observe. While there may be a small performance difference, it is probably at the level of a few percent. Certainly not a factor of more than 10. I see about a 50% reduction in speed when

Re: [gmx-users] FEP and loss of performance

Hi, This doesn't sound like normal behavior. In fact, this is not what I typically observe. While there may be a small performance difference, it is probably at the level of a few percent. Certainly not a factor of more than 10. You may want to provide an mdp file and topology, etc. so someone ca

Re: [gmx-users] FEP and loss of performance

I followed your suggestions and i tried to perform a MD run wit GROMACS and NAMD for dialanine peptide in a water box. The cell side cubic box was 40 A. GROMACS: With the free energy module there is a drop in gromacs performance of about 10/20 fold. Standard MD: Time: 6.693 6

Re: [gmx-users] FEP and loss of performance

Yes i am testing the possibility to perform an Hamiltonian-REMD Energy barriers can be overcome increasing the temperature system or scaling potential energy with a lambda value, these methods are "equivalent". Both have advantages and disavantages, at this stage it is not the right place to de

Re: [gmx-users] FEP and loss of performance

Chris Neale wrote: >> Dear Chris and Justin / Thank you for your precious suggestions />>/ This is a test that i perform in a single machine with 8 cores />>/ and gromacs 4.5.4. />>/ />>/ I am trying to enhance the sampling of a protein using the decoupling scheme />>/ of the free ener

Re: [gmx-users] FEP and loss of performance

Luca Bellucci wrote: Dear Chris and Justin Thank you for your precious suggestions This is a test that i perform in a single machine with 8 cores and gromacs 4.5.4. I am trying to enhance the sampling of a protein using the decoupling scheme of the free energy module of gromacs. However

Re: [gmx-users] FEP and loss of performance

Dear Chris and Justin Thank you for your precious suggestions This is a test that i perform in a single machine with 8 cores and gromacs 4.5.4. I am trying to enhance the sampling of a protein using the decoupling scheme of the free energy module of gromacs. However when i decouple only the

Re: [gmx-users] FEP and loss of performance

Luca Bellucci wrote: Hi Chris, thank for the suggestions, in the previous mail there is a mistake because couple-moltype = SOL (for solvent) and not "Protein_chaim_P". Now the problem of the load balance seems reasonable, because the water box is large ~9.0 nm. Now your outcome makes a lo

Re: [gmx-users] FEP and loss of performance

Hi Chris, thank for the suggestions, in the previous mail there is a mistake because couple-moltype = SOL (for solvent) and not "Protein_chaim_P". Now the problem of the load balance seems reasonable, because the water box is large ~9.0 nm. However the problem exist and the performance loss is v

Re: [gmx-users] FEP energy errors with positional restraints?

On 13/02/2011 6:07 PM, TJ Mustard wrote: On February 12, 2011 at 10:14 PM Mark Abraham wrote: On 13/02/2011 5:03 PM, TJ Mustard wrote: On February 12, 2011 at 9:31 PM Mark Abraham wrote: On 13/02/2011 3:57 PM, TJ Mustard wrote: On February 12, 20

Re: [gmx-users] FEP energy errors with positional restraints?

  On February 12, 2011 at 10:14 PM Mark Abraham wrote: On 13/02/2011 5:03 PM, TJ Mustard wrote:   On February 12, 2011 at 9:31 PM Mark Abraham wrote:

Re: [gmx-users] FEP energy errors with positional restraints?

On 13/02/2011 5:03 PM, TJ Mustard wrote: On February 12, 2011 at 9:31 PM Mark Abraham wrote: On 13/02/2011 3:57 PM, TJ Mustard wrote: On February 12, 2011 at 5:35 PM Mark Abraham wrote: On 13/02/2011 11:49 AM, TJ Mustard wrote: Hi all, I have bee

Re: [gmx-users] FEP energy errors with positional restraints?

  On February 12, 2011 at 9:31 PM Mark Abraham wrote: On 13/02/2011 3:57 PM, TJ Mustard wrote:   On February 12, 2011 at 5:35 PM Mark Abraham wrote:

Re: [gmx-users] FEP energy errors with positional restraints?

On 13/02/2011 3:57 PM, TJ Mustard wrote: On February 12, 2011 at 5:35 PM Mark Abraham wrote: On 13/02/2011 11:49 AM, TJ Mustard wrote: Hi all, I have been testing the ability of taking a sphere of a protein around a ligand, and positionally restrain the specified alpha carbons. I was

Re: [gmx-users] FEP energy errors with positional restraints?

  On February 12, 2011 at 5:35 PM Mark Abraham wrote: On 13/02/2011 11:49 AM, TJ Mustard wrote: Hi all,   I have been testing the ability of taking a sphere of a protein around a ligand, and positio

Re: [gmx-users] FEP energy errors with positional restraints?

On 13/02/2011 11:49 AM, TJ Mustard wrote: Hi all, I have been testing the ability of taking a sphere of a protein around a ligand, and positionally restrain the specified alpha carbons. I was hoping to keep non connected protein chains from drifting apart. I have been able to run these md/fe

Re: [gmx-users] FEP Calculation problem on GMX 4.5.1

I would have this in my production mdp files, or something like it:   ; Free energy control stuff free-energy  = yes    ; = no init-lambda  = XXX       ; = 0 delta-lambda = 0    ; = 0 foreign_lambda   =     ; =

Re: [gmx-users] FEP Calculation problem on GMX 4.5.1

TJ Mustard wrote: On October 20, 2010 at 9:22 PM "Marcelo Brandão" wrote: > Hello! > I am new to this list, probably someone has have the same problem I > am facing now with the use of Gromacs to calculate FEP (Free energy > pertubaion). > I've followed the gromacs tutorial for Free

Re: [gmx-users] FEP Calculation problem on GMX 4.5.1

On October 20, 2010 at 9:22 PM "Marcelo Brandão" wrote: > Hello! >  I am new to this list, probably someone has have the same problem I > am facing now with the use of Gromacs to calculate FEP (Free energy > pertubaion). > I've follow

Re: [gmx-users] FEP top file setup...

Ok I think I know where you are going with this. I started a small 2 nucleic acid system. I set RNA_Chain_A as the couple-moltype and couple-lambda0 and couple-lambda1 to vdw-q and none respectively. I then began a steep mdrun and got this error:     Program mdrun,

Re: [gmx-users] FEP top file setup...

- Original Message - From: TJ Mustard Date: Tuesday, September 14, 2010 10:54 Subject: [gmx-users] FEP top file setup... To: "gmx-users@gromacs.org" --- | > I am tryng to run free energy perturbation (FE

Re: [gmx-users] FEP for amino acid mutations

a LEU... Thank you for any hint you could give me! matteo > Date: Wed, 16 Jun 2010 15:17:30 +0200 > From: Matteo De Chiara > Subject: Re: [gmx-users] FEP for amino acid mutations. > To: gmx-users@gromacs.org > Message-ID: >         > Content-Type: text/plain; charset=ISO-8859-

Re: [gmx-users] FEP for amino acid mutations.

Thank you! I tried to change from Ala to Gly in aqueous environment and seems to have worked well. Now I will try to change a Trp, the amino acid I have to apply the real mutation. matteo > > Message: 5 > Date: Tue, 15 Jun 2010 08:53:25 +1000 > From: "Dallas B. Warren"

RE: [gmx-users] FEP for amino acid mutations.

I would make a new residue in the .rtp file. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 -

Re: [gmx-users] FEP dEkin/dlambda dG/dl constr. values continuously coming out 0.00000e+00

Those derivatives should be zero: the kinetic energy is determined by your thermostat and shouldn't change as a function of lambda - as it should for any normal free energy calculation in constant-temperature ensembles. Also, the constraint energy doesn't change as lambda changes (only the van de

Re: [gmx-users] FEP with bond formation, pair problem

David van der Spoel wrote: Berk Hess wrote: Hi, There are automatically different, since they are based on the A and B state charges and the A and B state atom types. But the problem is more complicated: Let's say there is a Butane radical C4H9. that you want to bond to another butane rad

Re: [gmx-users] FEP with bond formation, pair problem

Berk Hess wrote: Hi, There are automatically different, since they are based on the A and B state charges and the A and B state atom types. But the problem is more complicated: Let's say there is a Butane radical C4H9. that you want to bond to another butane radical to form octane (C8H18).

RE: [gmx-users] FEP with bond formation, pair problem

Hi, There are automatically different, since they are based on the A and B state charges and the A and B state atom types. Berk > Date: Thu, 19 Nov 2009 16:15:52 +0100 > From: joc...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: [gmx-users] FEP with bond formation, pair problem > > Hi

Re: [gmx-users] FEP problem with lambda perturbation 1 to 0.95

I agree with Carsten. See perhaps the discussion at www.alchemistry.org as well. On Fri, Aug 7, 2009 at 2:35 AM, Carsten Kutzner wrote: > On Aug 6, 2009, at 10:57 PM, Ragnarok sdf wrote: > > I am performing FEP do obtain the dimerization of a protein in >> membrane. The lambda intervals i am us

Re: [gmx-users] FEP problem with lambda perturbation 1 to 0.95

On Aug 6, 2009, at 10:57 PM, Ragnarok sdf wrote: I am performing FEP do obtain the dimerization of a protein in membrane. The lambda intervals i am using are 0.05 for each window. After that I rerun each lambda .trr perturbing the system (plus)0.05 and (minus)0.05 lambda value. Then with g-energ

Re: [gmx-users] FEP source code

a grep -rl -e "FEP" -e "dvdlambda" * in the gromacs source directory will show you these files. Carsten On Apr 24, 2009, at 4:33 PM, murat cetinkaya wrote: Hello GMX-people I am trying to locate the source code files regarding free energy perturbation (FEP) calculations. Does anyone have

Re: [gmx-users] FEP : separating components of dgdl

Hi This warning is really strange. You could try to execute grompp with -pp to get the preprocessed topology and have a look, if the the B-parameters are included correctly. As far as I know, it should; I do it the same way. Anyway, you could also explicitly take the parameters for that dihedra

Re: [gmx-users] FEP trajectory errors

Yep, all atoms begin to freezeeven the ones not being perturbed (i.e. the water molecules). It's pretty strange. It only happens for lambda=1.0. Below is my .mdp file. ; Run Control integrator = md ; calculation type dt = 0.0015

Re: [gmx-users] FEP trajectory errors

Do really all atoms "freeze". So also the atoms, which are not perturbed? Can you post your mdp-file? Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 231

Re: [gmx-users] FEP trajectory errors

The distortion was occuring because my position restraint potential was too weak. Increasing the force constant keeps the base in the right conformation. I believe my topology is correct, but it seems that turning off the VdW parameters causes the base to distort. I will look into this more. Also

Re: [gmx-users] FEP trajectory errors

Robert A value for alpha of 0.5 should work, although I tested some different alphas with different test systems and I have to say, that a proper value can be between 0.2 and 0.7 depending on the system itself. The distortion, you describe is really strange. I calculated DNA and single bases a

Re: [gmx-users] FEP trajectory errors

Thank you David and Maik for your detailed replies. Yes, I am trying to obtain an absolute free energy of binding. My thermodynamic cycle is: NT+DNA(adsorbed) -> NT+ DNA(desorbed) (obviously this is not the one that I'm obtaining with the alchemic method) Thus, the one I'm using in the simulatio

Re: [gmx-users] FEP trajectory errors

Robert, > I'm computing the free energy of binding of a DNA base on a carbon > nanotube. I think it's a pretty simple calculation and I'm proceeding > in a very standard way. This is what I'm doing: An absolute free energy? This isn't necessarily straightforward -- there are a lot of wrinkles. So

Re: [gmx-users] FEP trajectory errors

Robert I think, I cant help you too much, cause your problem involves too many sources of errors. Your topology (if continued that way) seems to be ok. Your TI-params seem to be ok, too. First, make clear: Do you use Position RESTRAINTS or (distance) CONSTRAINTS. There is a fundamental differ

Re: [gmx-users] FEP

[EMAIL PROTECTED] wrote: Hi, I would like to perform free energy perturbation using gromacs. I found some tutorial about this type of calculation, but a question is not clear. My calculation is very similar to the calculation described in the tutorial, because I want to change only the non bonde

Re: [gmx-users] FEP method in protein-ligand systems

Thank you David, I really appreciated your help. I will read your paper and try to go on. Thank you very much! 2007/7/27, David Mobley <[EMAIL PROTECTED]>: > > Hi, > > > I am trying to run some simulations in attempts to calculate binding > free > > energy between ligands and a protein using the F

Re: [gmx-users] FEP method in protein-ligand systems

Hi, > I am trying to run some simulations in attempts to calculate binding free > energy between ligands and a protein using the FEP method, but until now I > did not have any success. I have been looking for bibliography over this > subject, but, as you may know, there aren't many works about FEP

Re: [gmx-users] FEP and soft-core potentials

ECTED] on behalf of David Mobley Sent: Tue 7/24/2007 5:00 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] FEP and soft-core potentials Right. In fact, usually you would lose efficiency by using soft core potentials for an electrostatic transformation over doing it without soft core

RE: [gmx-users] FEP and soft-core potentials

-Original Message- From: [EMAIL PROTECTED] on behalf of David Mobley Sent: Tue 7/24/2007 5:00 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] FEP and soft-core potentials Right. In fact, usually you would lose efficiency by using soft core potentials for an electrostatic

Re: [gmx-users] FEP and soft-core potentials

Right. In fact, usually you would lose efficiency by using soft core potentials for an electrostatic transformation over doing it without soft core. The purpose of soft core is just to fix the problem with disappearing/inserting atoms which have 1/r^12 repulsion. David On 7/24/07, Georgios Pata

RE: [gmx-users] FEP with real or dummy charges?

Thanks again for the reply. A virtual point charge is what I want. Best wishes George -Original Message- From: [EMAIL PROTECTED] on behalf of Maik Goette Sent: Wed 5/23/2007 12:51 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] FEP with real or dummy charges? No

Re: [gmx-users] FEP with real or dummy charges?

From: [EMAIL PROTECTED] on behalf of Maik Goette Sent: Sat 5/19/2007 12:53 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] FEP with real or dummy charges? I don't really know, if this may solve your problem, but what I want to suggest is, not using PME for the simulation

RE: [gmx-users] FEP with real or dummy charges?

: [EMAIL PROTECTED] on behalf of Maik Goette Sent: Sat 5/19/2007 12:53 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] FEP with real or dummy charges? I don't really know, if this may solve your problem, but what I want to suggest is, not using PME for the simulation. I don't

Re: [gmx-users] FEP with real or dummy charges?

I don't really know, if this may solve your problem, but what I want to suggest is, not using PME for the simulation. I don't know, how other longerange-methods behave while changing the total charge of the system, PME won't work (as far, as I know). Concerning your way, how to perturb the cha

Re: [gmx-users] FEP softcore problematics

302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Berk Hess wrote: From: Maik Goette <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] FEP softco

Re: [gmx-users] FEP softcore problematics

Maik, The paper I'm talking about is by Anwar and Heyes and is the first entry here: http://scholar.google.com/scholar?hl=en&lr=&q=anwar+heyes+charge&btnG=Search Thank you for the detailed answer. It sounds reasonable. :) For sure it's the best way to make the calculations separatly and sum u

Re: [gmx-users] FEP softcore problematics

From: Maik Goette <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] FEP softcore problematics Date: Wed, 21 Jun 2006 14:55:34 +0200 Hi David Thank you for the detailed answer. It sounds reasonable. :) Fo

Re: [gmx-users] FEP softcore problematics

Hi David Thank you for the detailed answer. It sounds reasonable. :) For sure it's the best way to make the calculations separatly and sum up the energies at the end. You mentioned, that, in the case of splitting, the "density" of snapshot samplings at lambda=0,1 can be lower. So I guess, one r

Re: [gmx-users] FEP softcore problematics

Maik, You may be having the infamous "charge overlap" problem. In particular, one additional reason not to change LJ interactions at the same time as electrostatics is if you are inserting or disappearing atoms. Assume, for a moment, that you are disappearing a couple of atoms. The soft core for

RE: [gmx-users] fep calculation of L-Asn - D-Asn transition

From: Alexandra Patriksson <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] fep calculation of L-Asn - D-Asn transition Date: Wed, 24 May 2006 11:11:38 +0200 Dear all, I'm trying to do a fep calculation of the L to D transition o

Re: [gmx-users] FEP and position restraints

Right. Thank you for help. Now it works fine. :) - Original Message - From: "Berk Hess" <[EMAIL PROTECTED]> To: Sent: Thursday, April 06, 2006 6:02 PM Subject: RE: [gmx-users] FEP and position restraints From: "P" <[EMAIL PROTECTED]> Reply-To: D

RE: [gmx-users] FEP and position restraints

From: "P" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Subject: [gmx-users] FEP and position restraints Date: Thu, 6 Apr 2006 17:52:10 +0200 Hi all I'm doing FEP calculation on Zn ions. Is three a way to put position restraints on perturbated / dummy atoms. When I de

Re: [gmx-users] FEP

P, I am not sure what's going on; it could be any number of things. However, I would probably start by trying to create a topology which will work for free_energy=no (which corresponds to lambda=0 which corresponds to no perturbation (at least in the case when soft core is not used)). If your topo

Re: [gmx-users] FEP

Hi, are you using soft core portentials? Despite the theoretical drawbacks (see the previous discussion), the creation/annihilation of atoms was impossible (in my experience) without those potentials. Regards. Pedro. Hi all. I'm trying FEP In gromacs3.3. My system (3nm; 3nm; 3nm) consists o

Re: [gmx-users] FEP

Mark, > I am rather nervous about doing FEP/TI for disappearing charged> molecules, as it is not at all clear to me that it is possible do this > correctly with current methods. Perhaps someone else may be able to> comment more, but at least with long range electrostatics (PME), systems> are requir

Re: [gmx-users] FEP

Hi David, I am not an expert in FEP, but I have used that method to try to answer the following question: if there was a free energy difference between a system with a Na+ ion inserted by the best-potential method or randomly. I performed a series of MD runs (several lambdas) with annihilation

Re: [gmx-users] FEP

David Mobley wrote: I am rather nervous about doing FEP/TI for disappearing charged molecules, as it is not at all clear to me that it is possible do this correctly with current methods. Perhaps someone else may be able to comment more, but at least with long range electrostatics (PME), system

Re: [gmx-users] FEP

Hi, Hi all.I'm new to gromacs, and I would be glad to get some advice from more experienced usres.I would like to estimate the difference in free energy between two systems.  First system (A) consists of  DPPC membrane, TM-protein and some Zn ions interacting with the protein.  Second (B) ha