Re: [gmx-users] g_energy units

What (change in) free-energy difference are you trying to measure? How do these potential energy (differences) relate to them? Mark On Sat, Jun 29, 2013 at 7:13 PM, Leandro Bortot wrote: > Dear users, > is the energy output from g_energy really in kJ/mol? > > As an example, I wanted to

Re: [gmx-users] g_energy menu choices inconsistent?

On 02/10/12 11:53, Justin Lemkul wrote: Note that you can always select by name rather than number, i.e.: echo Temperature | g_energy -f ener.edr Didn't know that, this really saves me a lot of trouble! Thanks Justin! m. -- Massimo Sandal, Ph.D. http://devicerandom.org -- gmx-users mailing

Re: [gmx-users] g_energy menu choices inconsistent?

On 10/2/12 1:40 AM, Ladasky wrote: I have been trying to automate my simulation setup and monitoring. I wrote a script which calls g_energy, and automatically generates plots of potential energy from my EM step, temperature from my NVT equilibration step, and pressure and density from my NPT e

Re: [gmx-users] g_energy surf*surftens

Op 30 mar 2012 om 19:01 heeft "Payman Pirzadeh" het volgende geschreven: > Hello, > In calculation of the surf*surftension with g_energy, does this quantity > have any meaning when one deals with a protein in water(water fills up the > box)? Can it be indicative of the surface tension of protei

RE: [gmx-users] g_energy surf*surftens

Hello, In calculation of the surf*surftension with g_energy, does this quantity have any meaning when one deals with a protein in water(water fills up the box)? Can it be indicative of the surface tension of protein and water? Thanks. Paymon -- gmx-users mailing listgmx-users@gromacs.org ht

RE: [gmx-users] g_energy

Hello, I am using gromacs 4.5.4. In g_energy I see an option about #surf*surfTen. Could you please clarify how it is calculated? In a system with a protein and water, what does it correspond to? Best, Paymon -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...

Re: [gmx-users] g_energy Kinetic Energy

Hovakim Grabski wrote: Dear Gromacs users, After running two different simulations, one Hypercin molecule solvated in water and the other one with 2 Hypericin molecules solved in water as well. After that I used g_energy to extract the kinetic energy of the first simulation,but the values

Re: [gmx-users] g_energy for density calculation

On 4/02/2012 1:10 AM, Chrisostomos Batistakis wrote: On Fri, Feb 3, 2012 at 2:38 PM, Mark Abraham > wrote: On 4/02/2012 12:34 AM, Chrisostomos Batistakis wrote: Dear all I would like to calculate the total density vs time in my system during a

Re: [gmx-users] g_energy for density calculation

On Fri, Feb 3, 2012 at 2:38 PM, Mark Abraham wrote: > On 4/02/2012 12:34 AM, Chrisostomos Batistakis wrote: > > Dear all > > I would like to calculate the total density vs time in my system during an > NPT simulation. I read the manual that I have to use the g_energy command > in order to do that

Re: [gmx-users] g_energy for density calculation

On 4/02/2012 12:34 AM, Chrisostomos Batistakis wrote: Dear all I would like to calculate the total density vs time in my system during an NPT simulation. I read the manual that I have to use the g_energy command in order to do that. My problem is that when I am running: */ g_energy -f //a.

Re: [gmx-users] g_energy

Juliette N. wrote: Hello all, I have a quick question about extracting energy values from g_energy. I used an old trajectory to extend my simulation from 1 ns to 5 ns. Energy values from extended run do not take into account values of the first 1 ns. Is there any way to combine energies of

Re: [gmx-users] g_energy statistical information

Juliette N. wrote: Hello, I have a quick question about g_energy output. Can anyone descrive how the statistical info below are calculated? In literature I see for instance electrostatics is reported as: XXX + / - Y. Where Y is deviation or something like that. Which of the RMSD or Tot-

Re: [gmx-users] g_energy -ravg option

simon sham wrote: Hi, I need to calculate a running average on pressure, and have problem in using the -ravg option in g_energy command: I have tried the followings: 1. g_energy -f file.edr -ravg ravg.xvg -o pressure.xvg 2. g_energy -f file.edr -ravg -o pressure.xvg I could get the fluctuat

Re: [gmx-users] g_energy inconsistent results

On 8/03/2011 9:44 PM, Ehud Schreiber wrote: Dear Gromacs users, I am working with version 4.5.3, using the opls-aa forcefield in an implicit solvent, all-vs-all setting: pdb2gmx -ter -ff oplsaa -water none -f file.pdb I am energy-minimizing structures in 3 stages (steep, cg and l-bfgs). Th

Re: [gmx-users] g_energy: Energy names magic number mismatch

Mikhail Stukan wrote: Dear Justin and Berk, Thank you very much for the hint. Unfortunately, upgrade to 4.5.3 version doesn't solve the problem, diagnostic is still the same: == Program g_energy_d, VERSION 4.5.3 Source code file: ../../../src/gmxlib/enxio.c, line:

RE: Re: [gmx-users] g_energy: Energy names magic number mismatch

Dear Justin and Berk, Thank you very much for the hint. Unfortunately, upgrade to 4.5.3 version doesn't solve the problem, diagnostic is still the same: == Program g_energy_d, VERSION 4.5.3 Source code file: ../../../src/gmxlib/enxio.c, line: 422 Fatal error: Ener

Re: [gmx-users] g_energy: Energy names magic number mismatch

Mikhail Stukan wrote: Dear gromacs users, I am facing the following problem while running gromacs 4.5.1 at BlueGene/P supercomputer. The job is submitted by the following script file: #!/bin/sh # # @ account_no = xxx # @ job_name= NVT1 # @ job_type

RE: [gmx-users] g_energy: Energy names magic number mismatch

Hi, There have been some issues with version 4.5.1 and energy files and continuation. But I don't recall them being this fatal. Anyhow, it would be better to upgrade to version 4.5.3, which contains several bug fixes. Berk From: mstu...@slb.com To: gmx-users@gromacs.org Date: Wed, 8 Dec 2010

Re: [gmx-users] g_energy problem with 4.5.1 and 4.5.2

Hi Michael, I've been able to reproduce both problems - I'll fix them shortly. Sander On 2 Nov 2010, at 10:28 , Michael Brunsteiner wrote: > > Hi everybody, > > I run NPT simulations (with the double precision version of mdrun) of a > polymer melt > with anisotropic pressure scaling The sim

Re: [gmx-users] g_energy & graph .xvg

Thank you all, the xmgrace -nxy worked. but you're right, it's more useful to see the fluctuations. Thanks Carla On Tue, Jun 1, 2010 at 10:02 AM, Erik Marklund wrote: > Mark Abraham skrev: > > - Original Message - >> From: Carla Jamous >> Date: Tuesday, June 1, 2010 17:48 >> Subject

Re: [gmx-users] g_energy & graph .xvg

Mark Abraham skrev: - Original Message - From: Carla Jamous Date: Tuesday, June 1, 2010 17:48 Subject: [gmx-users] g_energy & graph .xvg To: Discussion list for GROMACS users Hi everyone, please I have a practical question that may sound stupid but I can't figure out the answer.

Re: [gmx-users] g_energy & graph .xvg

Carla Jamous skrev: Hi everyone, please I have a practical question that may sound stupid but I can't figure out the answer. When I run g_energy I type the Energies I need, for example: 10 (Potential) 14 (Kinetic) 12 (Total) My problem is even though I get the averages of the 3 energies on

Re: [gmx-users] g_energy & graph .xvg

- Original Message - From: Carla Jamous Date: Tuesday, June 1, 2010 17:48 Subject: [gmx-users] g_energy & graph .xvg To: Discussion list for GROMACS users > Hi everyone, > please  I have a practical question that may sound stupid but I can't figure > out the answer. > > When I run g_e

Re: [gmx-users] g_energy question

Marc Charendoff wrote: I am looking at the pairings for a given g-energy and see terms like: LJ-SR:C6Lrest LJ-LR:C6Lrest LJ-14:C6L-rest I know LJ, and SR, LR, 14. C6L is a ligand I am studying.What is a C6L-"rest" interaction? Guidance appreciated. The "rest" term refers to the

Re: [gmx-users] g_energy

leila karami wrote: Hi I want to use g_energy command. what means of 14 in LJ-14 or coulomb-14? Any help will highly appreciated! Please read the manual, especially sections regarding "1-4 interactions." -Justin -- Justin A. Lemkul Ph.D. Can

Re: [gmx-users] g_energy

Thanks allot for the ultrafast response and above all your help !. Arik Mark Abraham wrote: Arik Cohen wrote: Hi, Is there a way to tell the g_energy program the output option(i.e. Potential, Temperature ) in advance when you run the program. Namely, I would like to know if there is a

Re: [gmx-users] g_energy

Thanks allot for your ultrafast response and above all your help Arik On Mon, 09 Nov 2009 16:29:42 +1100 Mark Abraham wrote: Arik Cohen wrote: Hi, Is there a way to tell the g_energy program the output option(i.e. Potential, Temperature ) in advance when you run the program. Name

Re: [gmx-users] g_energy

Arik Cohen wrote: Hi, Is there a way to tell the g_energy program the output option(i.e. Potential, Temperature ) in advance when you run the program. Namely, I would like to know if there is a flag that I can give the program and thus skip the part when the g_energy program asks for an

Re: [gmx-users] g_energy and g_analyze give different averages

Ragnarok sdf wrote: When analysing FEP simulations. After running g_energy -f fep000.edr -f2 fep_000-005.edr for obtaining the dF = -kT ln < exp(-(EB-EA)/kT) >A I tried to obtain the standard deviation for this ensemble average using g_analyze -f runavg.xvg, but I've noticed that the average valu

Re: [gmx-users] g_energy=> Different Average values?

Chih-Ying Lin wrote: Hi After the command, g_energy -f abc.edr -o abc.xvg the average values is printed out on the screen. Energy Average RMSDFluct. Drift Tot-Drift Potential -267323 375.096 374.647 -0.12711-63.5543 Kinet

Re: [gmx-users] g_energy => the reasonable range of RMSD or Fluctuation ?

Hi Lin, That depends on the size of your system. Maybe add a book about statistical mechanics and thermodynamics to your reading list... Cheers, Tsjerk On Fri, Jun 19, 2009 at 8:00 PM, Chih-Ying Lin wrote: > HI > Once the system reaches the equilibrium, the thermal properties still > fluctuate

Re: [gmx-users] g_energy => RMSD = Standard Deviation?

Hi, It also doesn't hurt to read up more about statistics. The standard deviation is the square root of the second central moment of a distribution, so it's the expectation value for the average deviation found in a set of mutually indepent data points. Root mean square deviation does not imply mu

Re: [gmx-users] g_energy => RMSD = Standard Deviation?

Chih-Ying Lin wrote: HI After the command g_energy => the value of RMSD is shown, I can not find the math definition of RMSD from manual. Is the math definition of RMSD = Standard Deviation in Statistics? First Google result for "root mean square deviation": http://en.wikipedia.org/wiki/R

Re: [gmx-users] g_energy

Chih-Ying Lin wrote: Hi I have read the manual , Appendix C. After the command g_energy => Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -196428372

Re: [gmx-users] g_energy returns the instantaneous data or the average data?

Chih-Ying Lin wrote: Hi I want to calculate the pressure and the energy for the system. my .mdp file is as follows; writing out the energy and coordinates per 1000 steps. nstenergy = 1000 ; Writing out energy information every step nstxtcout = 1000 ; Writing coordinates every step Aft

Re: [gmx-users] g_energy non-interactive

Vitaly Chaban wrote: Hi, Is there a possibility to control g_energy output via command line without interactive selection? I have found nothing about this in the help message. We have a bunch of the alike systems, so we exactly know what numbers correspond to the wanted energy terms. If there

Re: [gmx-users] g_energy non-interactive

Vitaly Chaban wrote: Hi, Is there a possibility to control g_energy output via command line without interactive selection? I have found nothing about this in the help message. We have a bunch of the alike systems, so we exactly know what numbers correspond to the wanted energy terms. If there m

Re: [gmx-users] g_energy

[EMAIL PROTECTED] wrote: Hi, what's the difference among L-J(SR) and L-J(1-4), and among Coul.(SR), Coul (1-4) and Coul.-rec.. Thank you. L-J = Lennard-Jones Coul. = Coulomb SR = short-range 1-4 = read manual about 1-4 interactions Coul.-rec = reciprocal space contribution from PME For mor

Re: [gmx-users] g_energy

Hi, RMSD is your just deviation of backbone from native stare while RMS fluctuation shows the per atom deviation throughout simulation. regards, Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut

Re: [gmx-users] g_energy

Chih-Ying Lin wrote: Hi I use g_energy to calculate the total energy for the system. what is the unit for the total energy? and, how could I convert it to kJ/mole ? Values are always given in the standard units given in the manual. Energies are in kJ/mol. This information is printed out

回复： Re: [gmx-users] g_energy has no bond entry when MD analysis

Yes, I use bond constraints! Mark Abraham <[EMAIL PROTECTED]> 写道： > Dear friends: > when my MD was finished and I want to analyse the bond energy of the > protein ,but g_energy did not show bond entry: the first entry is angle? > When energy miniumzation finished,g_energy did show G96 bond. why?

Re: [gmx-users] g_energy has no bond entry when MD analysis

> Dear friends: > when my MD was finished and I want to analyse the bond energy of the > protein ,but g_energy did not show bond entry: the first entry is angle? > When energy miniumzation finished,g_energy did show G96 bond. why? So, when did you use bond length constraints? What effect would

RE: [gmx-users] g_energy -fee -inf problem

PROTECTED] on behalf of Mark Abraham Sent: Mon 24/09/2007 9:22 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_energy -fee -inf problem Naser, Md Abu wrote: > Hi Mark, > > The reacton shuld occur as: R-S-S-R + 2H+ -> 2R-SH. So at the very least, your "after&qu

Re: [gmx-users] g_energy -fee -inf problem

Naser, Md Abu wrote: Hi Mark, The reacton shuld occur as: R-S-S-R + 2H+ -> 2R-SH. So at the very least, your "after" topology will need to have these hydrogens... You can't just cleave the S-S bond out of the .top and expect it to work. Mark

RE: [gmx-users] g_energy -fee -inf problem

TED] on behalf of Mark Abraham Sent: Mon 24/09/2007 9:02 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_energy -fee -inf problem Naser, Md Abu wrote: > Hi Mark, > > Thank you very much for your replay.I was just trying to > calculate free energy difference between

Re: [gmx-users] g_energy -fee -inf problem

reduce them in a real system? Mark -Original Message- From: [EMAIL PROTECTED] on behalf of Mark Abraham Sent: Sat 22/09/2007 6:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_energy -fee -inf problem Naser, Md Abu wrote: > Hi All User, > > I am getting fr

RE: [gmx-users] g_energy -fee -inf problem

PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Mark Abraham Sent: Sat 22/09/2007 6:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_energy -fee -inf problem Naser, Md Abu wrote: > Hi

Re: [gmx-users] g_energy -fee -inf problem

Naser, Md Abu wrote: Hi All User, I am getting free energy difference -inf. 1st I run a protein in water molecule and then I made a different topology file with deleting 4 disulfide bonds and accordingly the angles and diherdal angles. What physical model are you trying to reproduce here? The

Re: [gmx-users] g_energy and pressure

Christopher Stiles wrote: I am trying to analyze the pressure of my box with respect to time using g_energy but it seems to give crazy numbers. For example it gives positive and negative numbers in the 1000’s. What units does it use or how does it calculate this? Should I be using another appli

Re: [gmx-users] g_energy doubt

There is a note above selection menu. "enter at a new line or 0" to end your selection. On 7/13/2007 9:12 AM, Mark Abraham wrote: Eduardo Martins Lopes wrote: Greetings all, I have this doubt about using g_energy to extract the box-x and box-y data from the energy.edr. The command i used is

Re: [gmx-users] g_energy doubt

Eduardo Martins Lopes wrote: Greetings all, I have this doubt about using g_energy to extract the box-x and box-y data from the energy.edr. The command i used is g_energy -f MDenergy.edr -ort orienttime.xvg -ora orientave.xvg and when i am prompted to choose wich data i want to retrieve, i type

Re: [gmx-users] g_energy sum

From: "merc mertens" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_energy sum Date: Mon, 30 Apr 2007 10:00:11 +0200 hello, you are right but "summing" over 1 term was done only fo

Re: [gmx-users] g_energy sum

"Berk Hess" <[EMAIL PROTECTED]> An: gmx-users@gromacs.org Betreff: Re: [gmx-users] g_energy sum > Hi, > > Well there is something special, in the sense that the sum is over > just one term, so summing does not make much sense. > But also in that case it should w

Re: [gmx-users] g_energy sum

users Subject: Re: [gmx-users] g_energy sum Date: Fri, 27 Apr 2007 13:41:11 +0200 Hi, If you haven't done anything special such as concatenating or cutting the energy file in parts after the simulation, I'd say it looks like a bug. Please create an entry at bugzilla.gromacs.org , uplo

Re: [gmx-users] g_energy sum

4000.00 -1129.730713 i think that the ener.edr only should contain only those steps listed in the xvg. cheers, merc Original-Nachricht Datum: Fri, 27 Apr 2007 13:04:04 +0200 Von: Erik Lindahl <[EMAIL PROTECTED]> An: Discussion list for GROMACS users Betreff: Re: [gmx

Re: [gmx-users] g_energy sum

r.edr only should contain only those steps listed in the xvg. cheers, merc Original-Nachricht Datum: Fri, 27 Apr 2007 13:04:04 +0200 Von: Erik Lindahl <[EMAIL PROTECTED]> An: Discussion list for GROMACS users Betreff: Re: [gmx-users] g_energy sum > Oops, > > S

Re: [gmx-users] g_energy sum

Oops, Sometimes it helps to read the mail. Mea culpa - forget my previous answer, this is something else. It could simply be a bug in g_energy; which version are you using, and what do you get if you remove "-b 2000" (i.e. include all steps)? Cheers, Erik On Apr 27, 2007, at 12:24 PM, m

Re: [gmx-users] g_energy sum

Hi, On Apr 27, 2007, at 12:24 PM, merc mertens wrote: the average energies from the log and the xvg do not match. does anybody know what is wrong here? thank you in advance, Nothing wrong. The statistics reported to stdout by g_energy is based on values from _all_ steps in the simulatio

Re: [gmx-users] g_energy

mahbubeh zarrabi wrote: Dear GROMACS users I want to calculate free energy in complex,receptor and ligand .what are energy groups in md.mdp? protein,solution or protein,protein,solution thanks please read the manual, chapter 3 etc. then look on the gromacs wesbite for tutorials. _

Re: [gmx-users] g_energy

> Dear all > I want to calculate binding energy between of ligand > and receptor in complex file.how can i describ gqroups > in mdp file. Read the man page for make_ndx and experiment with it in order to learn how to define groups. Then you use those groups as energy groups (see the manual). Oh a

Re: [gmx-users] g_energy

Dmitriy Golubobsky wrote: Dear GMX developers, and the question is: what kind if interactions consists, for example term LJ-(SR) he is equal for =LJ-SR:Poly-Poly+LJ-SR:Poly-SOL+LJ-SR:SOL-SOL or not? If the union of Poly and SOL are the whole system, then yes, the above relation should be true

Re: [gmx-users] g_energy info

On Wed, 2006-12-13 at 11:24 +0100, anna artese wrote: > Hi, > I'm a PhD italian student and I'm learning to use Gromacs software. I > used g_energy to calculate protein-protein energy for HIV-1 reverse > transcriptase, but I was wondering what's the meaning of Coul-SR or > Coul-LR terms. Hi, afai