[gmx-users] g_energy

Hello. I was calculating the viscosity of hexane through the Gromacs command g_energy. Three files are generated: visco.xvg, evisco.xvg and eviscoi.xvg. The file visco.xvg presents the shear viscosity and bulk, but the value does not match the experimental. I used 8 ns simulation at equilibrium. Ho

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

[gmx-users] g_energy units

Dear users, is the energy output from g_energy really in kJ/mol? As an example, I wanted to know which isoform of a protein forms the most stable dimer. I calculated the potential energy of the interaction between two monomers of the dimer and I got -2000 kJ/mol for one isoform and -4000

[gmx-users] g_energy -nbmin -nbmax options

Hi everyone, I am trying to calculate error of total energy in edr file using -nbmin -nbmax options. -nbmax 5 is giving 3% error while -nbmax 3000 gives an error of 0.91. Can one arbitrarily pick a large -nbmax to obtain less error? g_energy -f*.edr -nmol X -b XXX -o -nbmin 5 -nbmax 5 Energy

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

[gmx-users] g_energy menu choices inconsistent?

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 equilibration step. For each of these t

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

[gmx-users] g_energy Kinetic Energy

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 are  pretty high (it's abou

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.

[gmx-users] g_energy - what is COMPull En

Dear Gromacs users, I did pulling simulation and found COMPull En to give major contribution to my potential Energy, EPot. What is calculated by COMPull En? Thanks a lot in advance, Ilona Baldus -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

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

[gmx-users] g_energy

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 these two runs? or I shoul

[gmx-users] g_energy unable to -skip

Hello When I try to specify -skip with g_energy it still outputs the data from all frames into the .xvg file. I have to use eneconv -dt to strip out the data from said .edr (which yields a lot of "data not found" error messages) in order to get a compacted .xvg dataset... -- ===

[gmx-users] g_energy

Hello, the g_energy tool in Gromacs 4.0.7 provides calculation of viscosity (-vis) and surface tension (-o surften): a) Both, the shear and bulk viscosity are calculated with -vis tool. What are the equations for calculating them? In the manual, there is only the equation for the shear viscosi

[gmx-users] g_energy

Hello, the g_energy tool in Gromacs 4.0.7 provides calculation of viscosity (-vis) and surface tension (-o surften): a) Both, the shear and bulk viscosity are calculated with -vis tool. What are the equations for calculating them? In the manual, there is only the equation for the shear viscosi

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-

[gmx-users] g_energy statistical information

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-Drift is giving Y ? g_energy

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

[gmx-users] g_energy -ravg option

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 fluctuations in pressure.xvg, b

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

[gmx-users] g_energy inconsistent results

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). The last stage is the following: grompp

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

2010 13:50:21 + Subject: [gmx-users] g_energy: Energy names magic number mismatch 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

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

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= bluegene # @ output

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

[gmx-users] g_energy problem with 4.5.1 and 4.5.2

Hi everybody, I run NPT simulations (with the double precision version of mdrun) of a polymer melt with anisotropic pressure scaling The simulation seems to go fine, and the trajectories look reasonable, but there's something wrong with my g_energy output. === With 4.5.1 I get weird values

[gmx-users] g_energy output

Dear all, I have run a CG-MD simulation and output energies of different energy groups. When I run g_energy to get some of the energy terms out I input the number of molecules in my system -nmol "X" (X = Y number of water molecules (beads) + Z number of proteins + W number of lipids), to make sure

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

te: 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. >&g

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 t

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 answe

[gmx-users] g_energy & graph .xvg

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 my screen, I can't get th

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

[gmx-users] g_energy question

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. Thanks, Marc-- gmx-users mailing listgmx-users@groma

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

[gmx-users] g_energy

Hi I want to use g_energy command. what means of 14 in LJ-14 or coulomb-14? Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please

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

[gmx-users] g_energy

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 input for the Pote

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

[gmx-users] g_energy and g_analyze give different averages

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 values are quite different

[gmx-users] g_energy=> Different Average values from the screen than calculation of .xvg?

Hi After the command, g_energy -f abc.edr -o abc.xvg the average values is printed out on the screen. EnergyAverage RMSDFluct. Drift Tot-Drift Potential -267323 375.096 374.647 -0.12711 -63.5543 Kinetic En. 51901.5 259.034

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

Hi I have read through the manual but could not get it. Would you please explain it more? Thank you Lin 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. Dr

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

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

Hi After the command, g_energy -f abc.edr -o abc.xvg the average values is printed out on the screen. Energy Average RMSD Fluct. Drift Tot-Drift Potential -267323 375.096 374.647 -0.12711 -63.5543 Kinetic En. 51901.5 259.034 259.015 -0.02151 -10.7574 Total Energy -215421 275.52 274.683 -0.148

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

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

HI Once the system reaches the equilibrium, the thermal properties still fluctuate within some range. What is the reasonable/trustable range of RMSD or Fluctuation of those thermal properties ? Thank you Lin ___ gmx-users mailing listgmx-users@grom

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

[gmx-users] g_energy => RMSD vs Fluctuation

Hi The definition of the Fluctuation is shown on the Manual, Appendix C, eqn (C.1) The definition of the RMSD is as shown from the link. http://en.wikipedia.org/wiki/Root_mean_square_deviation The definition of the estimators is unclear though. So, what is the definition of the estimators? The fo

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

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

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? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org ht

[gmx-users] g_energy => both instantaneous and average

Hi I have read throught the Appendix C. The following is the .mdp file. Type the command g_energy -f abc-NVT500.edr -o abc-NVT500.xvg choose Pressure Based on my understanding of the Appendix C => g_energy will print out the instantaneous Pressure every 1000 step and save it into abc-NVT500.xv

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

[gmx-users] g_energy

Hi I have read the manual , Appendix C. After the command g_energy => Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -196428372.215340.8525.1803

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

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

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 After entering g_energy comman

Re[2]: [gmx-users] g_energy non-interactive

Justin, It great! Vitaly JAL> 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 numbe

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

[gmx-users] g_energy non-interactive

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 many alike systems it's

[gmx-users] g_energy

Dear all gmx users and developers, I selected the option 1, which is BOND in g_energy analyzation. I was then obtain a graph of bond energy (the graph is similar to potential energy graph). So, i am wonder what is the meaning of the graph? Another question is: what can we obtain or explain by t

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

[gmx-users] g_energy

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. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www

Re: [gmx-users] g_energy

  --- On Sat, 6/9/08, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: From: [EMAIL PROTECTED] <[EMAIL PROTECTED]> Subject: [gmx-users] g_energy To: gmx-users@gromacs.org Date: Saturday, 6 September, 2008, 2:41 PM Hi, how does it count the drift in g_energy? What is the equation?

[gmx-users] g_energy

Hi, how does it count the drift in g_energy? What is the equation? What is the difference among fluct. and RMSD? Thanks, see you soon. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the

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

[gmx-users] g_energy

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 ? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gm

[gmx-users] g_energy to compute free energy difference

Dear users, As the Gromacs manual mentioned, "g_energy" cauld calculate the free energy difference with an ideal gas state. After a simulation of protein in water with GMX3.3.1, I have tried the following commands to compute deltaG. 1. g_energy -f md.edr -fee -fetemp 300 -o energy1.xvg 2. g

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

[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? Please help me! Thank you! -

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

[gmx-users] g_energy -fee -inf problem

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. Then, I run -rerun for the both and and g_energy -fee, which giving me free energy

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

[gmx-users] g_energy and pressure

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 application to look at this? Addi

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

[gmx-users] g_energy doubt

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 "Box-X Box-Y" and nothing seem

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

[gmx-users] g_energy sum

hello, when i calculate energies with g_energy -f (ener.edr) -b 2000 -sum -o (energy.xvg) e.g. i get this average in the log: Statistics over 101 steps [ 2000. thru 4000. ps ], 1 data sets Energy Average RMSD Fluct. Drift Tot-Drift

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