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
po
thank you so much Mr.justin
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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 methyldiethan
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 10
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
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 at
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--
Gr
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 histogra
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 replica
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 c
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 hav
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, volum
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, of
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
equili
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 equilibratio
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 us
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, w
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 used
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
---
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
---
Potenti
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 is still positive
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
>> around 1000 kj/mol
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 ca
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 gen
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 Cur
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 on
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
minimzation.
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 c
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 me
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 scan for organic molecule u
Hi gromacs users,
How to do potential energy surface scan for organic molecule using Gromacs?
What are the steps?
Thanks,
Neha
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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 of the components
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
pheno
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 pa
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 G
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 would like to know wea
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 anything
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
;
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 PME and PBC while
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
Thank you. Should I not use PME and PBC while performing simulations in
Vaccum ?
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*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 oth
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 earl
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
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
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 w
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 wrote:
>
> https:
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 wrote:
> Dear
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 that I am getting with g_b
ct: 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 anyon
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
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> 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
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 partiti
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 Tot
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
--
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
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 energyminimization
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
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 m
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 check
Hi,
There's something catastrophically wrong with your input structure. Look it
with a visualization program, e.g. VMD, PyMol
Mark
On Thu, Feb 18, 2016 at 10:39 AM Subhashree Rout <
subhashree.r...@kiitbiotech.ac.in> wrote:
> Hii
>
> I am simulating protein (PfCDPK5) in water. After performing
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 em.mdp
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 of
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 wrote:
> Hi Mark,
>
> What do you mean by saying "thing"? Is phase changing?
>
> I visualized
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
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 wrote:
> Hi all,
>
> My system has 560 water molecules covered by 50 organic molecules. I run
> the simulation for
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/l9mJesD,ggDDZtb#0 (first pic)
I just could not understand what is going on after 7.5 ns?
Also I am doing this simulation to calcul
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 lin
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 to
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
Potent
Dear Bogdan,
Actually I have generated CNT from a garphene sheet myself. The last
question reflects that!
Thanks alot for answering all the questions and useful points you
mentioned.
Regards,
Mah
On Tue, Jan 20, 2015 at 10:43 PM, mah maz wrote:
> Dear Justin,
>
> Thank you very much for your b
On Fri, Jan 16, 2015 at 2:56 PM, mah maz 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
to read a bit mo
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 wrote:
> Hi Justin,
> I haven't come to a conclusion yet and need your help! I attached
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
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
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
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!
Rega
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 number
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 wrote:
> I see! You are right. But my syste
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 ar
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 wrote:
> Thank you Justin!
> you mean we can have a stable system with positive potential and total
> energy?
> Regards,
> Mah
>
> On Sun, Jan 1
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. Lemkul
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 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
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.
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
On 8/13/14, 1:28 AM, Meenakshi Rajput wrote:
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?
No idea what that means.
And in next positional restrained run and md simulation, charmm settin
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 at
Thanks a lot Justin.
On Aug 11, 2014 10:36 PM, "Meenakshi Rajput"
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 > wrote:
>
>> Thanks..but if
On 8/11/14, 1:06 PM, Meenakshi Rajput 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.
The proper settings (in Gromacs 5.0) for CHARMM36 are:
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = fo
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
wrote:
> Thanks..but if potential becomes positive after energy minimisation run,
> then is it normal or there
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 s
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" wrote:
> hi users
> i have run energy minimisation
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;
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
les
On 12/28/13, 2:12 AM, Ali Alizadeh wrote:
Dear Justin,
Thank you very much for your reply.
One point, why useless??? You meant this potential calculation is useless?
It's useless because no force field has been derived to reproduce such a value.
"The potential energy of a molecule" is us
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 wrote:
>
> Dear All users,
>
> I have a question about calculation of potential energy for an especial
> group. I know I ha
ot;
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
&
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 no
26. Dezember 2013 um 14:04 Uhr
*Von:* "Justin Lemkul"
*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 someth
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 not this means I must perform my
simulation agai
run across something showing perfect sinusoidal energy graphs of waters/solvent...but the trajectory used contained 5 ions and a single proteinDMSO is a tiny molecule...
Stephan
Gesendet: Donnerstag, 26. Dezember 2013 um 14:04 Uhr
Von: "Justin Lemkul"
An: gmx-us...@gromacs.org
Bet
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 it across the
run. Additionally, fluctua
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