Re: [gmx-users] potential energy doesn't have negative value

Den 2020-03-15 kl. 00:59, skrev Justin Lemkul: On 3/14/20 7:15 PM, Afsane Farhadi wrote: I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the

Re: [gmx-users] potential energy doesn't have negative value

thank you so much Mr.justin  Sent from Yahoo Mail on Android On Sun, Mar 15, 2020 at 3:38, Justin Lemkul wrote: On 3/14/20 8:05 PM, Afsane Farhadi wrote: > what do I have to do for solving this mater? I want to use a opls as > forcefield.  how can I find that forcefield for

Re: [gmx-users] potential energy doesn't have negative value

what do I have to do for solving this mater? I want to use a opls as forcefield.  how can I find that forcefield for methyldiethanolamine? Sent from Yahoo Mail on Android On Sun, Mar 15, 2020 at 3:29, Justin Lemkul wrote: On 3/14/20 7:15 PM, Afsane Farhadi wrote: > I generate a box of

Re: [gmx-users] potential energy doesn't have negative value

On 3/14/20 8:05 PM, Afsane Farhadi wrote: what do I have to do for solving this mater? I want to use a opls as forcefield.  how can I find that forcefield for methyldiethanolamine? http://zarbi.chem.yale.edu/ligpargen/ -Justin Sent from Yahoo Mail on Android On Sun, Mar 15, 2020 at

Re: [gmx-users] potential energy doesn't have negative value

On 3/14/20 7:15 PM, Afsane Farhadi wrote: I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the potential energy is positive.  the mdp file is

[gmx-users] potential energy doesn't have negative value

I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the potential energy is positive.  the mdp file is attached. Sent from Yahoo Mail on Android--

Re: [gmx-users] Potential Energy Distribution Plots in REMD

On 8/9/19 10:14 PM, Shan Jayasinghe wrote: Dear Gromacs Users, I want to plot potential energy distribution plot using the normal distribution curve (bell curve) for all replicas in my REMD simulation. I used the command, gmx analyze -f Penergy.xvg -dist -normalize However, I got a

Re: [gmx-users] Potential Energy Distribution Plots in REMD

I think you have to give (bandwidth) -bw 0.01 or any number according your data in your command line. On Sat, Aug 10, 2019, 07:45 Shan Jayasinghe wrote: > Dear Gromacs Users, > > I want to plot potential energy distribution plot using the normal > distribution curve (bell curve) for all

[gmx-users] Potential Energy Distribution Plots in REMD

Dear Gromacs Users, I want to plot potential energy distribution plot using the normal distribution curve (bell curve) for all replicas in my REMD simulation. I used the command, gmx analyze -f Penergy.xvg -dist -normalize However, I got a histogram, instead of a bell curve. Appreciate, if you

Re: [gmx-users] potential energy per molecules or per mole

I already answered your question. If you prefer words like "extensive thermodynamic property," please consider your favorite equations from thermodynamics, in which a linear function of energies, values of PV or TS are present. On the other side, despite the fact that all of these equations

Re: [gmx-users] potential energy per molecules or per mole

Dear Alex, Thank you for your response. I agree with all your statements. My issues are with units. In the first case, should it be kJ (total energy), as it is the Total potential energy_of the system_? Total energy of the system is an extensive thermodynamic property. I mean, for example,

Re: [gmx-users] potential energy per molecules or per mole

The potential energy _of the system_ is reported, and that's directly proportional to the number of molecules you have in your box. Energy per mole is a unit regardless of the number of molecules. After you properly rescale the total energy with the number of molecules, you still get kJ/mol,

[gmx-users] potential energy per molecules or per mole

Greetings! I am confused about the units of potential energy in gromacs. I have performed simulations of pure monoethanol (MEA) systems with certain parameters. The three systems I simulated consisted of 2400, 2800, and 3200 molecules of MEA, respectively, at 298 K and 1 bar. After reaching

[gmx-users] potential energy

Hi all GMX usersI did MD simulation under NPT ensembel. I evaluated potential energy during energy minimization, equilibration, and productionMD steps.  The plot of  potential energy indicates the nice, steady convergence of potentialenergy during energy minimization step. The first

Re: [gmx-users] Potential energy reported by gmx energy command

If I am not wrong, you are suggesting the "per mol" in KJ/mol is total number of particles in the system. Which in special case for pure component system should give per particle energy scaled by Avogadro number, so for my case the RMSD decrease by (N)^1/2 should come out to be same whether I

Re: [gmx-users] Potential energy reported by gmx energy command

Den 2018-07-04 kl. 11:19, skrev atb files: Thanks Prof. David, now my energies are making some sense and they are following the trend that, with increase in particle number RMSD decreases by (N)^1/2 for LJ fluid. If -nmol option is available, which may be used to calculate per particle averages,

Re: [gmx-users] Potential energy reported by gmx energy command

Thanks Prof. David, now my energies are making some sense and they are following the trend that, with increase in particle number RMSD decreases by (N)^1/2 for LJ fluid. If -nmol option is available, which may be used to calculate per particle averages, why default unit of "KJ/mol" has been

Re: [gmx-users] Potential energy reported by gmx energy command

Den 2018-06-28 kl. 09:03, skrev atb files: Hello experts, I did a LJ particles simulation, where I simulated two systems, 100 particle and 400 particle. For 100 particles energy is: Energy  Average   Err.Est.   RMSD  Tot-Drift

[gmx-users] Potential energy reported by gmx energy command

Hello experts, I did a LJ particles simulation, where I simulated two systems, 100 particle and 400 particle. For 100 particles energy is: Energy       Average   Err.Est.   RMSD  Tot-Drift ---

Re: [gmx-users] Potential energy

On 3/20/18 7:15 PM, Alex wrote: Thanks Justin. On Tue, Mar 20, 2018 at 3:02 PM, Justin Lemkul wrote: On 3/20/18 2:40 PM, Alex wrote: Dear all, The potential energy of my system after two minimization steps (with and without constrained) is converging well, however, it

Re: [gmx-users] Potential energy

Thanks Justin. On Tue, Mar 20, 2018 at 3:02 PM, Justin Lemkul wrote: > > > On 3/20/18 2:40 PM, Alex wrote: > >> Dear all, >> >> The potential energy of my system after two minimization steps (with and >> without constrained) is converging well, however, it is still positive >>

Re: [gmx-users] Potential energy

On 3/20/18 2:40 PM, Alex wrote: Dear all, The potential energy of my system after two minimization steps (with and without constrained) is converging well, however, it is still positive around 1000 kj/mol ! I think it is not a good sign for my system, but, what could be the reason and how I

[gmx-users] Potential energy

Dear all, The potential energy of my system after two minimization steps (with and without constrained) is converging well, however, it is still positive around 1000 kj/mol ! I think it is not a good sign for my system, but, what could be the reason and how I can overcome the issue? The system

Re: [gmx-users] Potential energy coming out to be zero but not negative

Dear Shayantani, The output you quote show a negative potential energy. Is that not for the run you refer to? (With regards to “Hello Sir”, may I suggest a more gender inclusive greeting.) Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska

Re: [gmx-users] Potential energy coming out to be zero but not negative

Noone knows if you can continue your equilibration with this result, but it has nothing to do with the sign of the total energy. In the case of biomolecular forcefields involving quadratic energy terms for bonded stuff, the sign of the total energy is meaningless. _Reduction_ in total energy

[gmx-users] Potential energy coming out to be zero but not negative

Hello Sir, When I go for energy minimization for a protein complex containing 3 proteins, I obtain potential energy being minimized upto zero from positive. The potential energy is not becoming negative even after running for many steps as viewed in potential.xvg obtained after energy

Re: [gmx-users] POTENTIAL ENERGY SURFACE SCAN

On 6/16/17 6:16 AM, Neha Gupta wrote: Thank you for the reply. I am given to understand that, we are supposed to run em.mdp and md.mdp file for the organic molecule of interest. After that, we are supposed to run mdrun -s md.tpr -rerun configuration.pdb What are the factors should we take

Re: [gmx-users] POTENTIAL ENERGY SURFACE SCAN

Thank you for the reply. I am given to understand that, we are supposed to run em.mdp and md.mdp file for the organic molecule of interest. After that, we are supposed to run mdrun -s md.tpr -rerun configuration.pdb What are the factors should we take care of while running md.mdp? How do we

Re: [gmx-users] POTENTIAL ENERGY SURFACE SCAN

Hi, Generate your configurations with some other tool, put them in a trajectory file, and use http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy Mark On Fri, 16 Jun 2017 11:13 Neha Gupta wrote: > Hi gromacs users, > > How to do potential energy surface

[gmx-users] POTENTIAL ENERGY SURFACE SCAN

Hi gromacs users, How to do potential energy surface scan for organic molecule using Gromacs? What are the steps? Thanks, Neha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] potential energy of a system

Dear Mark and Justin, Thanks a lot for the information On 29 March 2017 at 18:33, Justin Lemkul wrote: > > > On 3/29/17 8:43 AM, Mark Abraham wrote: > >> Hi, >> >> The total potential energy has everything by definition, so I don't know >> what you're asking. >> >> Additivity

Re: [gmx-users] potential energy of a system

On 3/29/17 8:43 AM, Mark Abraham wrote: Hi, The total potential energy has everything by definition, so I don't know what you're asking. Additivity of the components of the potential energy is an artefact of the construction of the model physics. While it is true that different physical

Re: [gmx-users] potential energy of a system

Hi, The total potential energy has everything by definition, so I don't know what you're asking. Additivity of the components of the potential energy is an artefact of the construction of the model physics. While it is true that different physical phenomena underlie some of the components, the

[gmx-users] potential energy of a system

Dear users, Which terms are included in the total potential energy of a system? Does it have COUL-SR and LJ-SR only, or does it also include the 1-4 terms? Thanks in advance. Regards, Saumyak -- *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's

Re: [gmx-users] Potential Energy is positive on minimizing the system

Thanks a lot! *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Feb 23, 2017 at 9:10 PM, Justin Lemkul wrote: > > > On 2/23/17 9:07 AM, Anurag Dobhal wrote: > >> Dear Justin, >> >> I

Re: [gmx-users] Potential Energy is positive on minimizing the system

On 2/23/17 9:07 AM, Anurag Dobhal wrote: Dear Justin, I would like to know weather the parameters below are correct for NVT equilibiration whicle doig a simulation in vaccum ? define = -DPOSRES ; position restrain the protein If you don't have solvent, there's no reason to restrain

Re: [gmx-users] Potential Energy is positive on minimizing the system

Dear Justin, I would like to know weather the parameters below are correct for NVT equilibiration whicle doig a simulation in vaccum ? define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ;

Re: [gmx-users] Potential Energy is positive on minimizing the system

Thank you ! *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Feb 23, 2017 at 7:09 PM, Justin Lemkul wrote: > > > On 2/23/17 8:29 AM, Anurag Dobhal wrote: > >> Thank you. Should I not use

Re: [gmx-users] Potential Energy is positive on minimizing the system

On 2/23/17 8:29 AM, Anurag Dobhal wrote: Thank you. Should I not use PME and PBC while performing simulations in Vaccum ? No, you should not. Use no PBC and infinite cutoffs (all cutoffs set to zero) to mimic vacuum conditions. Otherwise you're simulating some type of diffusely occupied

Re: [gmx-users] Potential Energy is positive on minimizing the system

Thank you. Should I not use PME and PBC while performing simulations in Vaccum ? -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or

Re: [gmx-users] Potential Energy is positive on minimizing the system

On 2/23/17 8:23 AM, Anurag Dobhal wrote: Dear gromacs users, I am Simulating a polymer chain having 20 monomer units. I am doing the simulation in the vaccum (I am not solvating the system). The total charge in my polymer chain is +9 and I am not nutrealizing the system as I was suggested

[gmx-users] Potential Energy is positive on minimizing the system

Dear gromacs users, I am Simulating a polymer chain having 20 monomer units. I am doing the simulation in the vaccum (I am not solvating the system). The total charge in my polymer chain is +9 and I am not nutrealizing the system as I was suggested earlier that if we are simulating a system in a

[gmx-users] Potential Energy is positive on minimizing the system

Dear gromacs users, I am Simulating a polymer chain having 20 monomer units. I am doing the simulation in the vaccum (I am not solvating the system). The total charge in my polymer chain is +9 and I am not nutrealizing the system as I was suggested earlier that if we are simulating a system in a

Re: [gmx-users] Potential energy in Zwanzig relationship

Take a look at how the python code does EXP. The information you want is in the dhdl.xvg. Look at the documentation for this file, and read the header. Come back with specific questions about the file if the header and documentation are not enough. On Fri, Feb 10, 2017 at 6:47 AM, gozde ergin

Re: [gmx-users] Potential energy in Zwanzig relationship

Dear Michael. Thanks for the reply. I have already used this python code however I would like to calculate myself by using the potential energies. Because I need to reweigh the free energy by using exponential re-weighting technique. > On 10 Feb 2017, at 14:44, Michael Shirts

Re: [gmx-users] Potential energy in Zwanzig relationship

https://github.com/MobleyLab/alchemical-analysis Takes gromacs dhdl.xvg output and calculate free energies by many different methods, including BAR, MBAR and Zwanzig. See http://www.alchemistry.org/wiki/Main_Page for more information. On Fri, Feb 10, 2017 at 5:26 AM, gozde ergin

[gmx-users] Potential energy in Zwanzig relationship

Dear all, I run thermodynamic integration simulation with gromacs and got the free energy by g_bar command. I also would like to estimate this free energy by using Zwanzig relationship of \DeltaG = -RT ln (_i Here U is the potential energy, right? However the results

Re: [gmx-users] Potential energy of each atom

zhe...@mail.iggcas.ac.cn>: > > Subject: Re: [gmx-users] Potential energy of each atom > > Message-ID: <56eba4a9.8020...@xray.bmc.uu.se> > > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > On 18/03/16 03:40, ??? wrote: > > > Dear all, >

[gmx-users] Potential energy of each atom

Dear all, Could anyone tell me how can I output potential energy of each atom from a trajectory file? All the best, Zhengcai Iggcas, CAS -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Potential energy of each atom

> Subject: Re: [gmx-users] Potential energy of each atom > Message-ID: <56eba4a9.8020...@xray.bmc.uu.se> > Content-Type: text/plain; charset=UTF-8; format=flowed > > On 18/03/16 03:40, ??? wrote: > > Dear all, > > > >Could anyone tell me how can

Re: [gmx-users] Potential energy of each atom

On 18/03/16 03:40, 张正财 wrote: Dear all, Could anyone tell me how can I output potential energy of each atom from a trajectory file? What does that mean? If you have a Na+ and a Cl- in the gas phase Gromacs can compute Coulomb energy and Lennard Jones energy. But how would you

Re: [gmx-users] potential energy between 2 energy group

On 3/3/16 2:12 AM, Tushar Ranjan Moharana wrote: Hi Everyone, I want to calculate potential energy between 2 coils of the same protein. I made 2 energy groups one for each coil and use gmx energy and got the following energy terms: Energy Average Err.Est. RMSD

[gmx-users] potential energy between 2 energy group

Hi Everyone, I want to calculate potential energy between 2 coils of the same protein. I made 2 energy groups one for each coil and use gmx energy and got the following energy terms: Energy Average Err.Est. RMSD Tot-Drift

Re: [gmx-users] Potential energy

On 2/21/16 3:35 PM, mohammad r wrote: Thank you Justin, do you know how I can find or modify the center of mass velocity of my system? During the run? If using comm-grps (you should for any system with PBC), then the COM velocity should be kept at or close to zero. You can confirm after

Re: [gmx-users] Potential energy

Thank you Justin, do you know how I can find or modify the center of mass velocity of my system? On Sunday, February 21, 2016 11:50 PM, Justin Lemkul wrote: On 2/21/16 3:15 PM, mohammad r wrote: > Hi everybody, > > > > Is it correct to say the potential energy after

Re: [gmx-users] Potential energy

On 2/21/16 3:15 PM, mohammad r wrote: Hi everybody, Is it correct to say the potential energy after energyminimization should be negative and in the order of 105-106 ?according to gromacs tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html

[gmx-users] Potential energy

Hi everybody,   Is it correct to say the potential energy after energyminimization should be negative and in the order of 105-106 ?according to gromacs tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html Thank you, Mohammad. -- Gromacs Users

Re: [gmx-users] Potential energy of protein after energy minimization

Hello Sir I have generated the structure using PHYRE server, performed its structural validations. As per your suggestion I have checked the protein in both visualizing software. During MD simulation of the protein, the pdb2gmx is generating topol.top and .itp without any errors. Do I need to

[gmx-users] Potential energy of protein after energy minimization

Hii I am simulating protein (PfCDPK5) in water. After performing energy minimization, the potential energy of my protein is 2.86082e+07. As mentioned in the tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html, the Epot should be negative. The

[gmx-users] Potential energy positive

Hi All, I am simulating molten urea (contains only urea molecule) at 406 K. After the energy minimization, I found the potential energy positive (~10^4 ). Steepest Descents converged to Fmax < 100 in 646 steps Potential Energy = 3.8694098e+04 Maximum force = 8.9818977e+01 on atom 26 Norm

Re: [gmx-users] Potential Energy-Umbrella sampling

I am using md-vv as an integrator but if I use m , I don't see this drift (movement) in my system. This is also another problem that I could not figure out. On Mon, Jun 15, 2015 at 6:04 PM, gozde ergin gozdeeer...@gmail.com wrote: Hi Mark, What do you mean by saying thing? Is phase changing?

Re: [gmx-users] Potential Energy-Umbrella sampling

Hi, Your trajectory went from one thing to a completely different thing, so what did your visual inspection of the trajectory tell you? Mark On Mon, 15 Jun 2015 17:54 gozde ergin gozdeeer...@gmail.com wrote: Hi all, My system has 560 water molecules covered by 50 organic molecules. I run

[gmx-users] Potential Energy-Umbrella sampling

Hi all, My system has 560 water molecules covered by 50 organic molecules. I run the simulation for 20 ns and here is my potential energy figure. http://imgur.com/DrBvnjs I just could not understand what is going on after 7.5 ns? Also I am doing this simulation to calculate the PMF. On the

Re: [gmx-users] Potential Energy-Umbrella sampling

Hi Mark, What do you mean by saying thing? Is phase changing? I visualized in VMD but could not manage to really captured the difference before 7.5 ns and after 7.5 ns. Also because during the simulation all bulk is moving in the box but distances between pullgroups stays constant so it is not

[gmx-users] potential energy is from energy mimization

Dear gmx, I am simulation a kinase protein which has (~1200 aa) length. When I energy minimize the protein with default em file from Justin A. Lemku tutorial. i have got the following output. writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 1162 steps

Re: [gmx-users] potential energy is from energy mimization

On 3/18/15 9:42 PM, Rj wrote: Dear gmx, I am simulation a kinase protein which has (~1200 aa) length. When I energy minimize the protein with default em file from Justin A. Lemku tutorial. i have got the following output. writing lowest energy coordinates. Steepest Descents converged

Re: [gmx-users] potential energy

On Fri, Jan 16, 2015 at 2:56 PM, mah maz mahma...@gmail.com wrote: These potential energies are the average ones, how can I get the final potential of the system? In the log file you get instantaneous values for all types of calculated energies. You can also get it with g_energy, but you'd have

Re: [gmx-users] potential energy

Dear Justin, Thank you very much for your beneficial analysis. The problem is not solved completely but the situation is improved for sure. Your help is always precious. Best Regards, Mah On 1/16/15, mah maz mahma...@gmail.com wrote: Hi Justin, I haven't come to a conclusion yet and need your

Re: [gmx-users] potential energy

On 1/16/15 8:56 AM, mah maz wrote: Hi Justin, I haven't come to a conclusion yet and need your help! I attached a copy of a typical g_energy -f ener.edr -o copied from terminal and an .mdp file. Bond18506.5 501625.68 -301.714 (kJ/mol) Angle

Re: [gmx-users] potential energy

Hi Justin, I haven't come to a conclusion yet and need your help! I attached a copy of a typical g_energy -f ener.edr -o copied from terminal and an .mdp file. Bond18506.5 501625.68 -301.714 (kJ/mol) Angle 9839.32 13580.506

Re: [gmx-users] potential energy

Hi Justin, That's right in the .edr I have more than these 4 terms, I just mentioned the terms related to energy of the system.The output file is a large one not in a proper format to be sent, but can be attached if possible. That was a great deal of help up to this point. Thank you very much!

Re: [gmx-users] potential energy

On 1/11/15 9:01 AM, mah maz wrote: Hi Justin, That's right in the .edr I have more than these 4 terms, I just mentioned the terms related to energy of the system.The output file is a large one Those aren't the only terms related to the energy, and conserved energy is actually a thermostat

Re: [gmx-users] potential energy

On 1/10/15 4:22 PM, mah maz wrote: I see! You are right. But my system is a nanotube not in gas phase. Is it possible in this case? Nanotube in some solvent? What do the various energy components show you? Remember, it's all additive, so you should be able to easily identify which terms

Re: [gmx-users] potential energy

On 1/10/15 4:39 PM, mah maz wrote: some solvent in nanotube actually! What do you mean by various energy components? In the results, I just have terms for potential, kinetic, total energy and conserved energy which are all positive in all steps. That's not possible. There are a large

Re: [gmx-users] potential energy

Thank you Justin! you mean we can have a stable system with positive potential and total energy? Regards, Mah On Sun, Jan 11, 2015 at 12:22 AM, mah maz mahma...@gmail.com wrote: Dear all, I wanted to know if the potential energy gained by g_energy -f ener.edr -o the total potential energy of

Re: [gmx-users] potential energy

I see! You are right. But my system is a nanotube not in gas phase. Is it possible in this case? Thanks alot! On Sun, Jan 11, 2015 at 12:40 AM, mah maz mahma...@gmail.com wrote: Thank you Justin! you mean we can have a stable system with positive potential and total energy? Regards, Mah

[gmx-users] potential energy

Dear all, I wanted to know if the potential energy gained by g_energy -f ener.edr -o the total potential energy of the system or partial ones like vdw energy. If it is the total energy, to my knowledge it should be negative, and its summation with the kinetic energy should be negative showing the

Re: [gmx-users] potential energy

On 1/10/15 4:10 PM, mah maz wrote: Thank you Justin! you mean we can have a stable system with positive potential and total energy? Sure. For example, gas-phase systems generally have positive potential energy. -Justin -- == Justin A.

Re: [gmx-users] potential energy

On 1/10/15 3:52 PM, mah maz wrote: Dear all, I wanted to know if the potential energy gained by g_energy -f ener.edr -o the total potential energy of the system or partial ones like vdw energy. If it is the total energy, to my knowledge it should be negative, It's the full potential energy.

Re: [gmx-users] potential energy

some solvent in nanotube actually! What do you mean by various energy components? In the results, I just have terms for potential, kinetic, total energy and conserved energy which are all positive in all steps. On Sun, Jan 11, 2015 at 12:52 AM, mah maz mahma...@gmail.com wrote: I see! You are

Re: [gmx-users] potential energy

Thanks a lot Justin. On Aug 11, 2014 10:36 PM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: thanks...can you help me out with the mdp file settings with charmm force field(proteins)? I am a new user to gromacs and stuck here. On Mon, Aug 11, 2014 at 5:07 AM, Meenakshi Rajput

Re: [gmx-users] potential energy

hi thanks for the charmm settings...but N atom and H atom of LYS 313 and ALA 364 are coming out of the complex. Can you tell me why is this happening? And in next positional restrained run and md simulation, charmm settings would be same or some difference should be there? On Tue, Aug 12, 2014

[gmx-users] potential energy

hi users i have run energy minimisation of docked complex by using this min.mdp:- cpp= /lib/cpp; Preprocessor include= -I../top; Directories to include in the topology format integrator= steep emtol= 1000; Stop minimization when the energy changes by

Re: [gmx-users] potential energy

On 8/11/14, 5:02 AM, Meenakshi Rajput wrote: hi users i have run energy minimisation of docked complex by using this min.mdp:- cpp= /lib/cpp; Preprocessor include= -I../top; Directories to include in the topology format integrator= steep emtol= 1000

Re: [gmx-users] potential energy

Thanks..but if potential becomes positive after energy minimisation run, then is it normal or there is some prblm with my mdp file. I used the same mdp file for this run also. I used charmm force field. On Aug 11, 2014 2:32 PM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: hi users i have run

Re: [gmx-users] potential energy

On 8/11/14, 8:07 AM, Meenakshi Rajput wrote: Thanks..but if potential becomes positive after energy minimisation run, then is it normal or there is some prblm with my mdp file. I used the same mdp file for this run also. I used charmm force field. For a condensed phase system, the potential

Re: [gmx-users] potential energy

thanks...can you help me out with the mdp file settings with charmm force field(proteins)? I am a new user to gromacs and stuck here. On Mon, Aug 11, 2014 at 5:07 AM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: Thanks..but if potential becomes positive after energy minimisation run, then

Re: [gmx-users] Potential energy calculations

:* Justin Lemkul jalem...@vt.edu *An:* gmx-us...@gromacs.org *Betreff:* Re: [gmx-users] Potential energy calculations On 12/26/13, 5:30 AM, lloyd riggs wrote: Zero it-- If you plot a potential energy value strait from the simulation it will be something like point a) -7000 point b) -7050 across

Re: [gmx-users] Potential energy

On 12/27/13, 6:00 PM, Ali Alizadeh wrote: Dear All users, I have a question about calculation of potential energy for an especial group. I know I had to define an energy group in .mdp file. I forgot to do it. I want to know can I extract this potential energy by post processing or not? If

Re: [gmx-users] Potential energy calculations

An:gmx-us...@gromacs.org Betreff:Re: [gmx-users] Potential energy calculations On 12/26/13, 4:52 PM, lloyd riggs wrote: Yes I know what you mean, however when your looking over a unit cell and trying to define a single molecule in the solvent (even as represented by the entire solvent makup), does

Re: [gmx-users] Potential energy

Dear Justin, Thank you very much for your reply. One point, why useless??? You meant this potential calculation is useless? On Sat, Dec 28, 2013 at 2:30 AM, Ali Alizadeh ali.alizadehmoja...@gmail.com wrote: Dear All users, I have a question about calculation of potential energy for an

Re: [gmx-users] Potential energy calculations

-users] Potential energy calculations On 12/26/13, 5:30 AM, lloyd riggs wrote: Zero it-- If you plot a potential energy value strait from the simulation it will be something like point a) -7000 point b) -7050 across a single simulation. Thus you have to find a beginning point and subtract

Re: [gmx-users] Potential energy calculations

Justin Lemkul wrote Gromacs reports energies in kJ per mole of equivalent systems. If you're looking for a value like configurational energy, use g_energy -nmol as needed to divide by the number of molecules in the system. -Justin On Mon, Dec 23, 2013 at 8:49 PM, virk lt; virkblitz@

[gmx-users] Potential energy calculations

Dear Users, I am try to simulate DMSO molecules. I am getting potential energy values of Energy Average Err.Est. RMSD Tot-Drift --- Potential -28160.8 4259.924

Re: [gmx-users] Potential energy calculations

Did you zero it ? Stephan Watkins Gesendet:Dienstag, 24. Dezember 2013 um 01:33 Uhr Von:virk virkbl...@yahoo.com An:gmx-us...@gromacs.org Betreff:[gmx-users] Potential energy calculations Dear Users, I am try to simulate DMSO molecules. I am getting potential energy values of Energy

Re: [gmx-users] Potential energy calculations

The potential energy of what exactly? The energy of bringing the atoms together to form a single DMSO molecule? If so then MD isn't appropriate for this type of calculation... On 24/12/13 00:33, virk wrote: Dear Users, I am try to simulate DMSO molecules. I am getting potential energy

Re: [gmx-users] Potential energy calculations

sorry, I didn't understand it what do you mean by zero it.But I have stabilised energy calculation for my simulation..I am thinking something wrong with units or something with my simulation -- View this message in context:

Re: [gmx-users] Potential energy calculations

I am trying to simulate mixture of DMSO and water at different mole fractionbut this value is for 100% DMSO. -- View this message in context: http://gromacs.5086.x6.nabble.com/Potential-energy-calculations-tp5013495p5013499.html Sent from the GROMACS Users Forum mailing list archive at