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

[David van der Spoel]

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 
potential energy is positive.  the mdp file is attached.


The mailing list does not accept attachments.

ATB does produce GROMOS-compatible force fields, but it is always up to 
the user to determine if the parameters are suitable. A positive 
potential energy means that the intermolecular interactions are weak 
compared to the intramolecular (bonded) interactions. You can use gmx 
energy or look in the .log file to see the various contributions to the 
total potential energy.


-Justin

The baseline oof the potential energy is not a meaningful number in 
classical force fields. You have to subtract 100 times the energy of the 
monomer, then you will have the enthalpy of vaporization (+/- kT) which 
you can compare to experiment.


--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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Re: [gmx-users] potential energy doesn't have negative value

[Afsane Farhadi]

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 methyldiethanolamine?

http://zarbi.chem.yale.edu/ligpargen/

-Justin

> 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 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.
> The mailing list does not accept attachments.
>
> ATB does produce GROMOS-compatible force fields, but it is always up to
> the user to determine if the parameters are suitable. A positive
> potential energy means that the intermolecular interactions are weak
> compared to the intramolecular (bonded) interactions. You can use gmx
> energy or look in the .log file to see the various contributions to the
> total potential energy.
>
> -Justin
>

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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

[Afsane Farhadi]

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 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.

The mailing list does not accept attachments.

ATB does produce GROMOS-compatible force fields, but it is always up to 
the user to determine if the parameters are suitable. A positive 
potential energy means that the intermolecular interactions are weak 
compared to the intramolecular (bonded) interactions. You can use gmx 
energy or look in the .log file to see the various contributions to the 
total potential energy.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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

[Justin Lemkul]

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 3:29, Justin Lemkul wrote:


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 attached.

The mailing list does not accept attachments.

ATB does produce GROMOS-compatible force fields, but it is always up to
the user to determine if the parameters are suitable. A positive
potential energy means that the intermolecular interactions are weak
compared to the intramolecular (bonded) interactions. You can use gmx
energy or look in the .log file to see the various contributions to the
total potential energy.

-Justin



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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

[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 potential energy is positive.  the 
mdp file is attached.


The mailing list does not accept attachments.

ATB does produce GROMOS-compatible force fields, but it is always up to 
the user to determine if the parameters are suitable. A positive 
potential energy means that the intermolecular interactions are weak 
compared to the intramolecular (bonded) interactions. You can use gmx 
energy or look in the .log file to see the various contributions to the 
total potential energy.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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

[Justin Lemkul]

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 histogram, instead of a bell curve.
Appreciate, if you could help me to get the normalised curve for potential
energy distribution.


gmx analyze produced what you asked for, a normalized histogram. You 
should not expect any given data series to necessarily follow a true 
normal distribution.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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

[Omkar Singh]

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 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 could help me to get the normalised curve for potential
> energy distribution.
>
> Thank you.
>
>
>
>
>
> --
> Best Regards
> Shan Jayasinghe
> --
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Re: [gmx-users] potential energy per molecules or per mole

[Alex]

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 have been traditionally rescaled to 1 mol, there is total mass 
of the system, i.e. what you call "extensive thermodynamic properties" 
are nothing but properties of a given amount of matter.


The same logic explains the difference between total volume and volume 
per mole. Your energy of intermolecular interactions is ~ 170 kJ/mol.


Alex


On 8/26/2018 10:12 PM, Dhawal Shah wrote:

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, volume. We have total volume of the system and volume
per mole. Both are different. If I say that 100 moles of water have 1000 m3
(Total volume_of the system_), and per mole, it is 10m3/mol. One is
system-size dependent and second one is not.

Regards,
Dhawal





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 course. In one case, it was per the entire system containing
N molecules, in the other it is per molecule. You do not weigh x kilos
per Dhawal, you just weigh x kilos.

Alex

On 8/26/2018 9:02 PM, Dhawal Shah wrote:

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
equilibrium, the potential energy of the systems (as computed from gmx
energy were)

Number of MEA molecules

MEA-MEA interaction energy (kJ/mol)

In pure MEA

2400

409523.0

2800

477119.5

3200

545348.3

How, can the potential energy (with units kJ/mol) be different for
different systems. It is all pure MEA, and the systems are in equilibrium.
Also the units is per mole. Energy per mole should be independent of the
number of molecules simulated?

However, if I divide the energy by the number of molecules, it is roughly
the same. 409523/2400 = 170.63; 477119.5/2800 = 170.39; 545348.3/3200 =
170.42. What is the unit now = kJ/mole/molecules?

If I want to understand the strength of interactions between MEA

molecules,

should I choose 170 kJ/mol/molecules or 409523 kJ/mol?

Regards,
Dhawal

*Dhawal Shah*


*Assistant Professor*
*Chemical Engineering Department*
*Nazarbayev University, Astana*

*Phone: +7 7172 70 9130 (O)*
*email: dhawal.s...@nu.edu.kz *


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

[Dhawal Shah]

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, volume. We have total volume of the system and volume
per mole. Both are different. If I say that 100 moles of water have 1000 m3
(Total volume_of the system_), and per mole, it is 10m3/mol. One is
system-size dependent and second one is not.

Regards,
Dhawal





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 course. In one case, it was per the entire system containing
N molecules, in the other it is per molecule. You do not weigh x kilos
per Dhawal, you just weigh x kilos.

Alex

On 8/26/2018 9:02 PM, Dhawal Shah wrote:
> 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
> equilibrium, the potential energy of the systems (as computed from gmx
> energy were)
>
> Number of MEA molecules
>
> MEA-MEA interaction energy (kJ/mol)
>
> In pure MEA
>
> 2400
>
> 409523.0
>
> 2800
>
> 477119.5
>
> 3200
>
> 545348.3
>
> How, can the potential energy (with units kJ/mol) be different for
> different systems. It is all pure MEA, and the systems are in equilibrium.
> Also the units is per mole. Energy per mole should be independent of the
> number of molecules simulated?
>
> However, if I divide the energy by the number of molecules, it is roughly
> the same. 409523/2400 = 170.63; 477119.5/2800 = 170.39; 545348.3/3200 =
> 170.42. What is the unit now = kJ/mole/molecules?
>
> If I want to understand the strength of interactions between MEA
molecules,
> should I choose 170 kJ/mol/molecules or 409523 kJ/mol?
>
> Regards,
> Dhawal
*Dhawal Shah*


*Assistant Professor*
*Chemical Engineering Department*
*Nazarbayev University, Astana*

*Phone: +7 7172 70 9130 (O)*
*email: dhawal.s...@nu.edu.kz *
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Re: [gmx-users] potential energy per molecules or per mole

[Alex]

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 course. In one case, it was per the entire system containing 
N molecules, in the other it is per molecule. You do not weigh x kilos 
per Dhawal, you just weigh x kilos.


Alex


On 8/26/2018 9:02 PM, Dhawal Shah wrote:

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
equilibrium, the potential energy of the systems (as computed from gmx
energy were)

Number of MEA molecules

MEA-MEA interaction energy (kJ/mol)

In pure MEA

2400

409523.0

2800

477119.5

3200

545348.3

How, can the potential energy (with units kJ/mol) be different for
different systems. It is all pure MEA, and the systems are in equilibrium.
Also the units is per mole. Energy per mole should be independent of the
number of molecules simulated?

However, if I divide the energy by the number of molecules, it is roughly
the same. 409523/2400 = 170.63; 477119.5/2800 = 170.39; 545348.3/3200 =
170.42. What is the unit now = kJ/mole/molecules?

If I want to understand the strength of interactions between MEA molecules,
should I choose 170 kJ/mol/molecules or 409523 kJ/mol?

Regards,
Dhawal


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

[atb files]

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 use or don't use 
-nmol option, or will the answer changes?  On Wed, 04 Jul 2018 15:37:15 
+0530 David van der Spoel  wrote  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, why default unit of "KJ/mol" has 
been used, which now looks very confusing. Please help Yogi  Because we 
typically simulation mixtures, e.g. 100 methanol and 100 water or 1 protein in 
water. Then we can not decompose into molecules any more. On Fri, 29 Jun 2018 
01:31:47 +0530 David van der Spoel  wrote  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 
--- 
Potential  0.126288  0.029   0.615731 -0.0324041  (kJ/mol) 
Kinetic En. 337.039   0.24    27.6568   0.443176  (kJ/mol) 
Total Energy    337.165   0.22    27.6615   0.410771  (kJ/mol) 
For 400 particle energy is: Energy  Average   Err.Est.  
 RMSD  Tot-Drift 
--- 
Potential  0.502517  0.042    1.34584   0.220501  (kJ/mol) 
Kinetic En.    1359   0.82    56.1468   -1.24836  (kJ/mol) 
Total Energy 1359.5   0.78    56.1548   -1.02787  (kJ/mol) 
Since both systems have exact same operating conditions, only particle number 
has been changed, the per particle energy should be same, right? Here I see the 
energies has become 4 times in the second case. Then what is meaning of 
reporting energies in "KJ/mol" ? There is nothing like my system is not fully 
equilibrated, I have thoroughly checked, the both systems are well 
equilibrated. Please help in understanding these energies. Thank you > gmx 
energy does not know what your system is composed of. However the -nmol 400 
flag may help. -- David van der Spoel, Ph.D., Professor of Biology Head of 
Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 
Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users 
mailing list * Please search the archive at 
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(un)subscribe requests visit 
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org. > -- David van der Spoel, Ph.D., 
Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala 
University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. 
http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive 
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Re: [gmx-users] Potential energy reported by gmx energy command

[David van der Spoel]

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, why default unit of "KJ/mol" has been used, which now looks very confusing. Please help Yogi  


Because we typically simulation mixtures, e.g. 100 methanol and 100 
water or 1 protein in water. Then we can not decompose into molecules 
any more.





On Fri, 29 Jun 2018 01:31:47 +0530 David van der Spoel 
 wrote  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 
--- 
Potential  0.126288  0.029   0.615731 -0.0324041  
(kJ/mol) Kinetic En. 337.039   0.24    27.6568   
0.443176  (kJ/mol) Total Energy    337.165   0.22    
27.6615   0.410771  (kJ/mol) For 400 particle energy is: 
Energy  Average   Err.Est.   RMSD  Tot-Drift 
--- 
Potential  0.502517  0.042    1.34584   0.220501  
(kJ/mol) Kinetic En.    1359   0.82    56.1468   
-1.24836  (kJ/mol) Total Energy 1359.5   0.78    
56.1548   -1.02787  (kJ/mol) Since both systems have exact same 
operating conditions, only particle number has been changed, the per 
particle energy should be same, right? Here I see the energies has 
become 4 times in the second case. Then what is meaning of reporting 
energies in "KJ/mol" ? There is nothing like my system is not fully 
equilibrated, I have thoroughly checked, the both systems are well 
equilibrated. Please help in understanding these energies. Thank you > 
gmx energy does not know what your system is composed of. However the 
-nmol 400 flag may help. -- David van der Spoel, Ph.D., Professor of 
Biology Head of Department, Cell & Molecular Biology, Uppsala 
University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. 
http://www.icm.uu.se -- Gromacs Users mailing list * Please search the 
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--
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Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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Re: [gmx-users] Potential energy reported by gmx energy command

[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, why default unit of "KJ/mol" has been used, 
which now looks very confusing. Please help Yogi  On Fri, 29 Jun 2018 
01:31:47 +0530 David van der Spoel  wrote  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 
--- 
Potential  0.126288  0.029   0.615731 -0.0324041  (kJ/mol) 
Kinetic En. 337.039   0.24    27.6568   0.443176  (kJ/mol) 
Total Energy    337.165   0.22    27.6615   0.410771  (kJ/mol) 
For 400 particle energy is: Energy  Average   Err.Est.  
 RMSD  Tot-Drift 
--- 
Potential  0.502517  0.042    1.34584   0.220501  (kJ/mol) 
Kinetic En.    1359   0.82    56.1468   -1.24836  (kJ/mol) 
Total Energy 1359.5   0.78    56.1548   -1.02787  (kJ/mol) 
Since both systems have exact same operating conditions, only particle number 
has been changed, the per particle energy should be same, right? Here I see the 
energies has become 4 times in the second case. Then what is meaning of 
reporting energies in "KJ/mol" ? There is nothing like my system is not fully 
equilibrated, I have thoroughly checked, the both systems are well 
equilibrated. Please help in understanding these energies. Thank you > gmx 
energy does not know what your system is composed of. However the -nmol 400 
flag may help. -- David van der Spoel, Ph.D., Professor of Biology Head of 
Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 
Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users 
mailing list * Please search the archive at 
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Re: [gmx-users] Potential energy reported by gmx energy command

[David van der Spoel]

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 
--- Potential 
 0.126288  0.029   0.615731 -0.0324041  (kJ/mol) Kinetic En.  
   337.039   0.24    27.6568   0.443176  (kJ/mol) Total Energy    
337.165   0.22    27.6615   0.410771  (kJ/mol) For 400 particle energy is: Energy 
 Average   Err.Est.   RMSD  Tot-Drift 
--- Potential 
 0.502517  0.042    1.34584   0.220501  (kJ/mol) Kinetic En.  
  1359   0.82    56.1468   -1.24836  (kJ/mol) Total Energy 
1359.5   0.78    56.1548   -1.02787  (kJ/mol) Since both systems have exact same 
operating conditions, only particle number has been changed, the per particle energy 
should be same, right? Here I see the energies has become 4 times in the second case. 
Then what is meaning of reporting energies in "KJ/mol" ? There is nothing like 
my system is not fully equilibrated, I have thoroughly checked, the both systems are well 
equilibrated. Please help in understanding these energies. Thank you

gmx energy does not know what your system is composed of. However the 
-nmol 400 flag may help.


--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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Re: [gmx-users] Potential energy

[Justin Lemkul]

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
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 generated via "gmx
insert-molecules" contains 1000 molecules of "C21H28O4".


Look at the individual values of internal (bonded) terms and nonbonded
terms. Likely the intermolecular interactions are fairly weak, and the
potential energy of the system is dominated by internal terms, which are by
definition positive.


I changed the minimization criteria, now I have a negative potential energy
around (-332 kj/mo), and below are the list of different energies: the
bond, angle and LJ/Coulomb-14 are positive. Do you think having a weak
intermolecular interactions is a problem for the system?
Energy  Average   Err.Est.   RMSD  Tot-Drift

---
Bond819.2869.2 27.407   -42.6564
(kJ/mol)
Angle   1948.894.49.80344-23.362
(kJ/mol)
Proper Dih. 252.261  0.011  0.0262872  0.0474904
(kJ/mol)
LJ-14   8356.141.2 2.4604   -7.05906
(kJ/mol)
Coulomb-14  5798.87   0.19   0.357136   -1.13575
(kJ/mol)
LJ (SR)-9800.04   0.11   0.219992  -0.772991
(kJ/mol)
Disper. corr.  -423.936  0  0  0
(kJ/mol)
Coulomb (SR)   -9722.23   0.15   0.284124   0.915601
(kJ/mol)
Coul. recip.267.995 0.0039  0.0126721  0.0266248
(kJ/mol)
Potential  -332.748 1539.6655   -75.3192
(kJ/mol)
Pres. DC  0  0  0  0  (bar)


I don't see any problems here.

-Justin



Regards,
Alex


Second question;

To calculate the RDF between pair of atoms, let's say A and B, I was
wondering if those two atoms should be differentiated in index.ndx file
from beginning before invoking the gmx gromps?(similar to energygrps) or
one can does the simulation without index.ndx and still possible to
calculate the RDF between those two atoms?


There is no need for anything like energygrps. If you want to exclude the
intramolecular contribution to the RDF (if relevant), you have to increase
nrexcl in the topology and generate a new .tpr, otherwise everything is
controlled by index groups.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
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Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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Re: [gmx-users] Potential energy

[Alex]

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 !
>> 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 generated via "gmx
>> insert-molecules" contains 1000 molecules of "C21H28O4".
>>
>
> Look at the individual values of internal (bonded) terms and nonbonded
> terms. Likely the intermolecular interactions are fairly weak, and the
> potential energy of the system is dominated by internal terms, which are by
> definition positive.
>
I changed the minimization criteria, now I have a negative potential energy
around (-332 kj/mo), and below are the list of different energies: the
bond, angle and LJ/Coulomb-14 are positive. Do you think having a weak
intermolecular interactions is a problem for the system?
Energy  Average   Err.Est.   RMSD  Tot-Drift

---
Bond819.2869.2 27.407   -42.6564
(kJ/mol)
Angle   1948.894.49.80344-23.362
(kJ/mol)
Proper Dih. 252.261  0.011  0.0262872  0.0474904
(kJ/mol)
LJ-14   8356.141.2 2.4604   -7.05906
(kJ/mol)
Coulomb-14  5798.87   0.19   0.357136   -1.13575
(kJ/mol)
LJ (SR)-9800.04   0.11   0.219992  -0.772991
(kJ/mol)
Disper. corr.  -423.936  0  0  0
(kJ/mol)
Coulomb (SR)   -9722.23   0.15   0.284124   0.915601
(kJ/mol)
Coul. recip.267.995 0.0039  0.0126721  0.0266248
(kJ/mol)
Potential  -332.748 1539.6655   -75.3192
(kJ/mol)
Pres. DC  0  0  0  0  (bar)


Regards,
Alex

>
> Second question;
>> To calculate the RDF between pair of atoms, let's say A and B, I was
>> wondering if those two atoms should be differentiated in index.ndx file
>> from beginning before invoking the gmx gromps?(similar to energygrps) or
>> one can does the simulation without index.ndx and still possible to
>> calculate the RDF between those two atoms?
>>
>
> There is no need for anything like energygrps. If you want to exclude the
> intramolecular contribution to the RDF (if relevant), you have to increase
> nrexcl in the topology and generate a new .tpr, otherwise everything is
> controlled by index groups.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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Re: [gmx-users] Potential energy

[Justin Lemkul]

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 can overcome the issue? The system generated via "gmx
insert-molecules" contains 1000 molecules of "C21H28O4".


Look at the individual values of internal (bonded) terms and nonbonded 
terms. Likely the intermolecular interactions are fairly weak, and the 
potential energy of the system is dominated by internal terms, which are 
by definition positive.



Second question;
To calculate the RDF between pair of atoms, let's say A and B, I was
wondering if those two atoms should be differentiated in index.ndx file
from beginning before invoking the gmx gromps?(similar to energygrps) or
one can does the simulation without index.ndx and still possible to
calculate the RDF between those two atoms?


There is no need for anything like energygrps. If you want to exclude 
the intramolecular contribution to the RDF (if relevant), you have to 
increase nrexcl in the topology and generate a new .tpr, otherwise 
everything is controlled by index groups.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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

[Erik Marklund]

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 Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 23 Feb 2018, at 19:32, SHYANTANI MAITI 
> wrote:

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.

Energy  Average   Err.Est.   RMSD  Tot-Drift

---
Potential-6.06412e+061.2e+06 5.5e+07 -7.26522e+06
(kJ/mol)

Is the energy minimization considerable for further equilibration or do I
need to obtain only negative energy and after that only should I start my
equilibration? Does the value of potential energy  obtained after
minimization need to be  negative in all cases? Can I continue my
equilibration with this result?

Thanking you

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

[Alex]

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 EM is a correct trend. Do consult the manual for the energy 
terms used in your forcefield.


Alex


On 2/23/2018 11:32 AM, SHYANTANI MAITI wrote:

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.

Energy  Average   Err.Est.   RMSD  Tot-Drift

---
Potential-6.06412e+061.2e+06 5.5e+07 -7.26522e+06
(kJ/mol)

Is the energy minimization considerable for further equilibration or do I
need to obtain only negative energy and after that only should I start my
equilibration? Does the value of potential energy  obtained after
minimization need to be  negative in all cases? Can I continue my
equilibration with this result?

Thanking you



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Re: [gmx-users] POTENTIAL ENERGY SURFACE SCAN

[Justin Lemkul]

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 care of while running md.mdp?

How do we mention the dihedral angle of our interest?

Could you please elucidate?



You need to generate a series of conformations as a function of the changing 
dihedral.  It's a bit tedious to do in GROMACS, but essentially, you apply 
[dihedral_restraints] to the configuration and then energy-minimize the 
structure.  Then, using a topology *without* restraints, simply calculate the 
single-point energy of the minimized structure.  Follow the link Mark provided 
closely.


-Justin



Thanks,
Neha







On Fri, Jun 16, 2017 at 2:39 PM, Mark Abraham 
wrote:


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 using

Gromacs?


What are the steps?

Thanks,
Neha
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Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
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Re: [gmx-users] POTENTIAL ENERGY SURFACE SCAN

[Neha Gupta]

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 mention the dihedral angle of our interest?

Could you please elucidate?


Thanks,
Neha







On Fri, Jun 16, 2017 at 2:39 PM, Mark Abraham 
wrote:

> 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 using
> Gromacs?
> >
> > What are the steps?
> >
> > Thanks,
> > Neha
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Re: [gmx-users] POTENTIAL ENERGY SURFACE SCAN

[Mark Abraham]

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 using Gromacs?
>
> What are the steps?
>
> Thanks,
> Neha
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Re: [gmx-users] potential energy of a system

[Saumyak Mukherjee]

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 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 parameterization of the
>> force field did not target meaningful decomposition of the potential
>> energy. But you might be able to benefit from fortuitous cancellation
>> effects when comparing such things.
>>
>>
> Nitpick here: in CHARMM (and our polarizable model), we seek to get a
> variety of QM interaction energies explicitly correct (interactions with
> water, ions, other small molecules) so indeed there is some reliability in
> these metrics with CHARMM.  Of course, like all force fields, there is some
> inherent error cancellation but we do make an effort to get all of this
> kind of stuff right. Most other force fields, of course, do not, seeking
> instead to get overall properties correct, leaving the details to be
> debatable.  We try to get it all :)
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 

*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

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

[Justin Lemkul]

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
phenomena underlie some of the components, the parameterization of the
force field did not target meaningful decomposition of the potential
energy. But you might be able to benefit from fortuitous cancellation
effects when comparing such things.



Nitpick here: in CHARMM (and our polarizable model), we seek to get a variety of 
QM interaction energies explicitly correct (interactions with water, ions, other 
small molecules) so indeed there is some reliability in these metrics with 
CHARMM.  Of course, like all force fields, there is some inherent error 
cancellation but we do make an effort to get all of this kind of stuff right. 
Most other force fields, of course, do not, seeking instead to get overall 
properties correct, leaving the details to be debatable.  We try to get it all :)


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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

[Mark Abraham]

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 parameterization of the
force field did not target meaningful decomposition of the potential
energy. But you might be able to benefit from fortuitous cancellation
effects when comparing such things.

Mark

On Wed, Mar 29, 2017 at 12:00 PM Saumyak Mukherjee <
mukherjee.saumya...@gmail.com> wrote:

> 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 Group
> Solid State and Structural Chemistry Unit
> Indian Institute of Science
> Bangalore - 560012
>
> Mob : 8017292426
> Alternative e-mail : saumyakmukher...@gmail.com
> smukher...@sscu.iisc.ernet.in
> 
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] Potential Energy is positive on minimizing the system

[Anurag Dobhal]

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 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.
> Normally one restrains the solute to allow the solvent to relax around it.
> Here, this serves no purpose.
>
> ; Run parameters
>> integrator = md ; leap-frog integrator
>> nsteps = 5 ; 2 * 5 = 100 ps
>> dt = 0.002 ; 2 fs
>> ; Output control
>> nstxout = 100 ; save coordinates every 0.2 ps
>> nstvout = 100 ; save velocities every 0.2 ps
>> nstenergy = 100 ; save energies every 0.2 ps
>> nstlog = 100 ; update log file every 0.2 ps
>> ; Bond parameters
>> continuation = no ; first dynamics run
>> constraint_algorithm = lincs ; holonomic constraints
>> constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
>> lincs_iter = 1 ; accuracy of LINCS
>> lincs_order = 4 ; also related to accuracy
>> ; Neighborsearching
>> ns_type = simple ; search neighboring grid cells
>>
>
> Note you also need cutoff-scheme = group here.
>
> nstlist = 0 ; 10 fs
>> rlist = 0.0 ; short-range neighborlist cutoff (in nm)
>> rcoulomb = 0.0 ; short-range electrostatic cutoff (in nm)
>> rvdw = 0.0 ; short-range van der Waals cutoff (in nm)
>> ; Electrostatics
>> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
>>
>
> As I said before, you can't use PME (grompp will fail anyway, because you
> can't have PME without PBC).  Use a plain cutoff.
>
> pme_order = 0 ; cubic interpolation
>> fourierspacing = 0.0 ; grid spacing for FFT
>> ; Temperature coupling is on
>> tcoupl = V-rescale ; modified Berendsen thermostat
>> tc-grps = Other ; two coupling groups - more accurate
>> tau_t = 0.1 ; time constant, in ps
>> ref_t = 300 ; reference temperature, one for each group, in K
>> ; Pressure coupling is off
>> pcoupl = no ; no pressure coupling in NVT
>> ; Periodic boundary conditions
>> pbc = no ; 3-D PBC
>> ; Dispersion correction
>> DispCorr = EnerPres ; account for cut-off vdW scheme
>>
>
> Dispersion correction is also not applicable.
>
> -Justin
>
> ; Velocity generation
>> gen_vel = yes ; assign velocities from Maxwell distribution
>> gen_temp = 300 ; temperature for Maxwell distribution
>> gen_seed = -1 ; generate a random seed
>>
>> Thank You
>>
>>
>>
>>
>> *Anurag Dobhal*
>> *Graduate Student (Bioprocess Technology)*
>> *Institute of Chemical Technology, Mumbai*
>> *Contact: +91 8898486877*
>>
>>
>> On Thu, Feb 23, 2017 at 7:23 PM, Anurag Dobhal <
>> anurag.dob...@nano-medicine.co.in> wrote:
>>
>> 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 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 crystal environment.


 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
 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 http://www.gromacs.org/Support/Mailing_Lists

 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.


>>>
>>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users 

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

[Justin Lemkul]

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.  Normally one 
restrains the solute to allow the solvent to relax around it.  Here, this serves 
no purpose.



; Run parameters
integrator = md ; leap-frog integrator
nsteps = 5 ; 2 * 5 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = simple ; search neighboring grid cells


Note you also need cutoff-scheme = group here.


nstlist = 0 ; 10 fs
rlist = 0.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.0 ; short-range electrostatic cutoff (in nm)
rvdw = 0.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics


As I said before, you can't use PME (grompp will fail anyway, because you can't 
have PME without PBC).  Use a plain cutoff.



pme_order = 0 ; cubic interpolation
fourierspacing = 0.0 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Other ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 300 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = no ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme


Dispersion correction is also not applicable.

-Justin


; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed

Thank You




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Feb 23, 2017 at 7:23 PM, Anurag Dobhal <
anurag.dob...@nano-medicine.co.in> wrote:


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 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 crystal environment.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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send a mail to gmx-users-requ...@gromacs.org.








--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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

[Anurag Dobhal]

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
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = simple ; search neighboring grid cells
nstlist = 0 ; 10 fs
rlist = 0.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.0 ; short-range electrostatic cutoff (in nm)
rvdw = 0.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 0 ; cubic interpolation
fourierspacing = 0.0 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Other ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 300 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = no ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed

Thank You




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Feb 23, 2017 at 7:23 PM, Anurag Dobhal <
anurag.dob...@nano-medicine.co.in> wrote:

> 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 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 crystal environment.
>>
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> 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 http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>

-- 


*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 other use is prohibited. If you 
have received this in error, please contact the sender and delete this 
material from your computer. Any comments or statements made herein do not 
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the email or accessing any attachments, please check and scan for virus.*
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Re: [gmx-users] Potential Energy is positive on minimizing the system

[Anurag Dobhal]

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 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 crystal environment.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> 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 http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>

-- 


*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 other use is prohibited. If you 
have received this in error, please contact the sender and delete this 
material from your computer. Any comments or statements made herein do not 
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the email or accessing any attachments, please check and scan for virus.*
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Re: [gmx-users] Potential Energy is positive on minimizing the system

[Justin Lemkul]

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 crystal environment.


-Justin

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==

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Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
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Health Sciences Facility II, Room 629
University of Maryland, Baltimore
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Re: [gmx-users] Potential Energy is positive on minimizing the system

[Anurag Dobhal]

Thank you. Should I not use PME and PBC while performing simulations in
Vaccum ?

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

[Justin Lemkul]

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 earlier that if we are  simulating a system in a vaccum we can
continue without neutralizing the system (https://www.mail-archive.com/
gromacs.org_gmx-users@maillist.sys.kth.se/msg23520.html).

Now when I am minimizing my system I am not getting negative potential
energy (Potential Energy  =  4.5656064e+03). I am using gromacs Version
4.6.5 and the parameters of the minim.mdp are below

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps = 5; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz  ; Periodic Boundary Conditions (yes/no)


Any help will be appreciated. Thank you



That's normal.  But your .mdp file is not truly in vacuo since you're using PME 
and PBC.  But you should expect a positive energy when there's no solvent.


-Justin

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Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
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Re: [gmx-users] Potential energy in Zwanzig relationship

[Michael Shirts]

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  wrote:

> 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://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 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_bar (82 kcal/mol) and with
> >> Zwanzig equation (406 kcal/mol) are totally different.
> >> Do anyone has an idea why I am getting that different results?
> >>
> >> Bests
> >> --
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Re: [gmx-users] Potential energy in Zwanzig relationship

[gozde ergin]

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://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 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_bar (82 kcal/mol) and with
>> Zwanzig equation (406 kcal/mol) are totally different.
>> Do anyone has an idea why I am getting that different results?
>> 
>> Bests
>> --
>> 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 http://www.gromacs.org/Support/Mailing_Lists
>> 
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>> 
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Re: [gmx-users] Potential energy in Zwanzig relationship

[Michael Shirts]

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 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_bar (82 kcal/mol) and with
> Zwanzig equation (406 kcal/mol) are totally different.
> Do anyone has an idea why I am getting that different results?
>
> Bests
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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Re: [gmx-users] Potential energy of each atom

[Josip Lovrić]

Potential energy for one atom is not well defined physical quantity as far
as I know, you can only calculate potential energy for at least two body
(atoms). You need to give more details about what you want and I do not
know what LAMMPS do.

Josip

2016-03-18 11:03 GMT+01:00 张正财 <zhangzhe...@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,
> > >
> > >Could anyone tell me how can I output potential energy of each
> atom from a trajectory file?
> > >
> > What does that mean?
>
> Like the command in LAMMPS, "compute pe/atom", I want to display the
> potential energy of each atom in simulation system. is it possible in
> gromacs?
> >
> > 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 partition that over
> > atoms?
> >
> >
> >
> > >All the best,
> > >
> > >   Zhengcai
> > >
> > >  Iggcas, CAS
> > >
> > >
> >
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> >
> >
>
>
>
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Re: [gmx-users] Potential energy of each atom

[张正财]

> 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 I output potential energy of each atom 
> > from a trajectory file?
> >
> What does that mean?

Like the command in LAMMPS, "compute pe/atom", I want to display the potential 
energy of each atom in simulation system. is it possible in gromacs?
> 
> 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 partition that over 
> atoms?
> 
> 
> 
> >All the best,
> >
> >   Zhengcai
> >
> >  Iggcas, CAS
> >
> >
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> 
> 



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

[David van der Spoel]

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 partition that over 
atoms?





   All the best,

  Zhengcai

 Iggcas, CAS





--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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Re: [gmx-users] potential energy between 2 energy group

[Justin Lemkul]

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-Drift
---
Coul-SR:coil1-coil2-85.75671.210.33425.15837  (kJ/mol)
LJ-SR:coil1-coil2  -22.9698   0.566.46579   -3.33975  (kJ/mol)
Coul-14:coil1-coil2  00.0  0.0 0.0
  (kJ/mol)
LJ-14:coil1-coil2  00.0 0.0  0.0
(kJ/mol)



*Now my doubt is can I say the addition of above energy is the net
potential energy between those 2 groups? Does this (Coul-SR) includes


It's the short-range interaction energy.  That may or may not reflect something 
that has any physical meaning.



hydrogen bond energy also? If not then how can I calculate it? *



Hydrogen bonds are primarily electrostatic in nature.  There's no discrete 
energy term for it, but it's included in what you've calculated.




*I used gmx hbond -temp 298 (298 is the temperature) after selecting groups
I got following result:*Hydrogen bond thermodynamics at T = 298 K
Fitting parameters chi^2 = 0.000649398
Q =  0
--
Type  Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward 0.022 45.795  14.000  0.000649398
Backward   -0.063-15.875-666.000
One-way 0.043 23.120  12.306
Integral   -0.039-25.489-666.000
Relaxation  0.052 19.113  11.835

*Can we calculate hydrogen bond energy from this? If not then what these
terms are.   *



I suggest you read the reference to the method you're trying to use before 
using it.

-Justin


Thanks for your valuable advice.



"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Re: [gmx-users] Potential energy

[Justin Lemkul]

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 the 
run with gmx traj -ov -com and select "System."


-Justin



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 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

 >

As a broad generalization, but strictly speaking, that's not always true.  A
comparable protein in a similarly sized box will probably have something on that
order, but that is by no means an absolute rule.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu  |
(410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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--
==

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Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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Re: [gmx-users] Potential energy

[mohammad r]

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 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
>

As a broad generalization, but strictly speaking, that's not always true.  A 
comparable protein in a similarly sized box will probably have something on 
that 
order, but that is by no means an absolute rule.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Potential energy

[Justin Lemkul]

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



As a broad generalization, but strictly speaking, that's not always true.  A 
comparable protein in a similarly sized box will probably have something on that 
order, but that is by no means an absolute rule.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

[Subhashree Rout]

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 the structure with other protein prediction server or
software for 3D structure?



On Thu, Feb 18, 2016 at 3:21 PM, Mark Abraham 
wrote:

> 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 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 file-
> > ; minim.mdp - used as input into grompp to generate em.tpr
> > integrator= steep; Algorithm (steep = steepest descent
> > minimization)
> > emtol= 1000.0  ; Stop minimization when the maximum force <
> > 1000.0 kJ/mol/nm
> > emstep  = 0.01  ; Energy step size
> > nsteps= 5  ; Maximum number of (minimization) steps
> to
> > perform
> >
> > ; Parameters describing how to find the neighbors of each atom and how to
> > calculate the interactions
> > nstlist= 1; Frequency to update the neighbor list
> > and long range forces
> > cutoff-scheme   = Verlet
> > ns_type= grid; Method to determine neighbor list
> > (simple, grid)
> > coulombtype= PME; Treatment of long range electrostatic
> > interactions
> > rcoulomb= 1.0; Short-range electrostatic cut-off
> > rvdw= 1.0; Short-range Van der Waals cut-off
> > pbc= xyz ; Periodic Boundary Conditions (yes/no)
> >
> > Kindly suggest where I am going wrong.
> >
> > --
> > Subhashree Rout
> > PhD Scholar
> > Bioinformatics Lab
> > KIIT School of Biotechnology
> > KIIT University
> > Bhubaneswar
> > Odisha
> > INDIA
> > Pin-751024
> > --
> > Gromacs Users mailing list
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> >
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>



-- 
Subhashree Rout
PhD Scholar
Bioinformatics Lab
KIIT School of Biotechnology
KIIT University
Bhubaneswar
Odisha
INDIA
Pin-751024
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Re: [gmx-users] Potential Energy-Umbrella sampling

[gozde ergin]

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?

 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 easy to capture
 what is going on there.

 On Mon, Jun 15, 2015 at 5:58 PM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

 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
  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 calculate the PMF. On the links there
  are two PMF curves for the same system for 4ns and 20ns. They are pretty
  different! (4 ns seems more realistic)
 
  http://imgur.com/l9mJesD,ggDDZtb#0 (second pic).
 
  What could be the reason to get two very different PMF curve for the
 same
  system?
 
  bests
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Re: [gmx-users] Potential Energy-Umbrella sampling

[Mark Abraham]

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
 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 calculate the PMF. On the links there
 are two PMF curves for the same system for 4ns and 20ns. They are pretty
 different! (4 ns seems more realistic)

 http://imgur.com/l9mJesD,ggDDZtb#0 (second pic).

 What could be the reason to get two very different PMF curve for the same
 system?

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

[gozde ergin]

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 easy to capture
what is going on there.

On Mon, Jun 15, 2015 at 5:58 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 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
  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 calculate the PMF. On the links there
  are two PMF curves for the same system for 4ns and 20ns. They are pretty
  different! (4 ns seems more realistic)
 
  http://imgur.com/l9mJesD,ggDDZtb#0 (second pic).
 
  What could be the reason to get two very different PMF curve for the same
  system?
 
  bests
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
 
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Re: [gmx-users] potential energy is from energy mimization

[Justin Lemkul]

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 Fmax  1000 in 1162 steps
Potential Energy  = -4.6686910e+06
Maximum force =  9.6213324e+02 on atom 10673
Norm of force =  1.6875889e+01

After i plot the potential and through  gmx energy -f em.edr -o potential.xvg 
 by selecting potential (15) and 0, i end up with following results..
Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Potential1.97914e+09  2e+09 5.83904e+10 -1.18272e+10  
(kJ/mol)



The average potential during EM has no use.





When i try to see this value in xmgrace plot, i ccouldnt see any plot. Doesnt 
mean my system is not relaxed well? Should i need to increase the steps of em ? 
if so, how do i ? Thanks.



Probably the potential just drops precipitously and the resulting scale is such 
that you can't clearly see it.  Look at the .xvg in a text editor and you will 
see the progression of the energy, or adjust the scale in Grace.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] potential energy

[Bogdan Costescu]

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
to read a bit more about its options :)

 Are average potentials good terms to decide if the
 simulation was wrong?

They can be, if you know what to expect. But you have to compare
apples with apples - a comparison of CNT plus some solvent to a
protein in water is not relevant. Furthermore, the force field that
you choose can make a big difference...

 Can the positive potentials be the effect of forcefield inappropriate files?

Only you can decide that :) We have no idea what force field you have
used and whether that force field is appropriate for what you intend
to do.

The truncated Morse potential we have developed for graphene does
result in positive potentials. In general, most/all potentials for
graphene/CNTs result in positive potential energies as the Coulomb
term is missing. This is due to the fact that the Coulomb term can't
possibly model the coupled while also very mobile electrons in
graphene/CNTs, and is normally just left undefined.

 The system is a CNT containing some solvent. Can positive potentials be the
 reflection of the system's angle pressure not willing to reform from plane
 graphene system?

I can't quite understand the last sentence. You mention your system is
a CNT, but now you talk about graphene and reformation. Are you hoping
to roll/unroll between graphene and CNTs???

Cheers,
Bogdan
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Re: [gmx-users] potential energy

[mah maz]

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 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   -30.2625
 (kJ/mol)
 Proper Dih. 60199.3 23845.936106.894
 (kJ/mol)
 LJ-14   40461.9 411748.27   -227.144
 (kJ/mol)
 Coulomb-140  0  0  0
 (kJ/mol)
 LJ (SR)-10117.72.6118.855   -3.85515
 (kJ/mol)
 Coulomb (SR)   -156.169  9 40.82335.6671
 (kJ/mol)
 Potential118733 741142.65   -420.414
 (kJ/mol)
 Kinetic En. 14932.17.3423.825   -50.1192
 (kJ/mol)
 Total Energy 133665 811221.66   -470.533
 (kJ/mol)
 Conserved En.180812 57121.277397.186
 (kJ/mol)
 Temperature 295.064   0.148.37495  -0.990376  (K)
 Pressure  -0.072961   0.17 17.163  -0.120159  (bar)
 Vir-XX  4860.4521021707.326.9299
 (kJ/mol)
 Vir-XY  4.732333.3 1176.9   -2.74323
 (kJ/mol)
 Vir-XZ  3.180977.51907.36 4.2031
 (kJ/mol)
 Vir-YX  4.731473.31176.89   -2.74818
 (kJ/mol)
 Vir-YY  5388.86 39 5500.8202.824
 (kJ/mol)
 Vir-YZ0.05093923.21101.973.89409
 (kJ/mol)
 Vir-ZX  3.180897.51907.364.19967
 (kJ/mol)
 Vir-ZY0.05142363.21101.973.89442
 (kJ/mol)
 Vir-ZZ  4871.7620021686.431.3387
 (kJ/mol)
 Pres-XX0.156061   0.2525.1574  -0.125195  (bar)
 Pres-XY  -0.00268517 0.00331.36879 0.00150158
 (bar)
 Pres-XZ  -0.00196111 0.00982.21263 -0.0154319
 (bar)
 Pres-YX  -0.00268417 0.00331.36879 0.00150732
 (bar)
 Pres-YY   -0.511872  0.0196.38934 -0.0849178  (bar)
 Pres-YZ  0.000542369 0.00171.27895 0.00355122
 (bar)
 Pres-ZX  -0.00196102 0.00982.21263 -0.0154279
 (bar)
 Pres-ZY  0.000541808 0.00171.27895 0.00355084
 (bar)
 Pres-ZZ0.136928   0.2425.1334  -0.150365  (bar)
 #Surf*SurfTen   8.815353.2359.945   -1.26863  (bar
 nm)
 T-CNT   295.063   0.148.44198  -0.997647  (K)
 T-grp1  295.202   0.2138.5349   0.485478  (K)
 T-grp2294.688   0.3253.7236   -2.39488  (K)



 dt  =  0.0001
 tinit   =  0
 nsteps  =  200
 nstxout =  1000
 nstvout =  1000
 nstfout =  0
 nstlog  =  1000
 nstenergy   =  1000
 nstlist =  5
 ns_type =  grid
 rlist   =  0.9
 coulombtype =  cutoff
 rcoulomb= 0.9
 rvdw=  0.9
 pbc = xyz
 integrator  = md-vv
 Tcoupl  =  nose-hoover
 tau_t   =  0.1 0.1 0.1
 ref_t   =  295 295 295
 tc_grps = CNT grp1 grp2
 gen_temp= 295

 Your answer to any of these questions would be a ton of help!
 These potential energies are the average ones, how can I get the final
 potential of the system? Are average potentials good terms to decide if the
 simulation was wrong?
 Can the positive potentials be the effect of forcefield inappropriate
 files?
 The system is a CNT containing some solvent. Can positive potentials be the
 reflection of the system's angle pressure not willing to reform from plane
 graphene system?

 I would appreciate your help. Many thanks in advance!
 Regards,
 Mah





 On Sun, Jan 11, 2015 at 5:31 PM, mah maz mahma...@gmail.com 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
 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!
 Regards,
 Mah


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Re: [gmx-users] potential energy

[Justin Lemkul]

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   9839.32 13580.506   -30.2625
(kJ/mol)
Proper Dih. 60199.3 23845.936106.894
(kJ/mol)
LJ-14   40461.9 411748.27   -227.144
(kJ/mol)
Coulomb-140  0  0  0
(kJ/mol)
LJ (SR)-10117.72.6118.855   -3.85515
(kJ/mol)
Coulomb (SR)   -156.169  9 40.82335.6671
(kJ/mol)
Potential118733 741142.65   -420.414
(kJ/mol)
Kinetic En. 14932.17.3423.825   -50.1192
(kJ/mol)
Total Energy 133665 811221.66   -470.533
(kJ/mol)
Conserved En.180812 57121.277397.186
(kJ/mol)
Temperature 295.064   0.148.37495  -0.990376  (K)
Pressure  -0.072961   0.17 17.163  -0.120159  (bar)
Vir-XX  4860.4521021707.326.9299
(kJ/mol)
Vir-XY  4.732333.3 1176.9   -2.74323
(kJ/mol)
Vir-XZ  3.180977.51907.36 4.2031
(kJ/mol)
Vir-YX  4.731473.31176.89   -2.74818
(kJ/mol)
Vir-YY  5388.86 39 5500.8202.824
(kJ/mol)
Vir-YZ0.05093923.21101.973.89409
(kJ/mol)
Vir-ZX  3.180897.51907.364.19967
(kJ/mol)
Vir-ZY0.05142363.21101.973.89442
(kJ/mol)
Vir-ZZ  4871.7620021686.431.3387
(kJ/mol)
Pres-XX0.156061   0.2525.1574  -0.125195  (bar)
Pres-XY  -0.00268517 0.00331.36879 0.00150158  (bar)
Pres-XZ  -0.00196111 0.00982.21263 -0.0154319  (bar)
Pres-YX  -0.00268417 0.00331.36879 0.00150732  (bar)
Pres-YY   -0.511872  0.0196.38934 -0.0849178  (bar)
Pres-YZ  0.000542369 0.00171.27895 0.00355122  (bar)
Pres-ZX  -0.00196102 0.00982.21263 -0.0154279  (bar)
Pres-ZY  0.000541808 0.00171.27895 0.00355084  (bar)
Pres-ZZ0.136928   0.2425.1334  -0.150365  (bar)
#Surf*SurfTen   8.815353.2359.945   -1.26863  (bar
nm)
T-CNT   295.063   0.148.44198  -0.997647  (K)
T-grp1  295.202   0.2138.5349   0.485478  (K)
T-grp2294.688   0.3253.7236   -2.39488  (K)



dt  =  0.0001
tinit   =  0
nsteps  =  200
nstxout =  1000
nstvout =  1000
nstfout =  0
nstlog  =  1000
nstenergy   =  1000
nstlist =  5
ns_type =  grid
rlist   =  0.9
coulombtype =  cutoff
rcoulomb= 0.9
rvdw=  0.9
pbc = xyz
integrator  = md-vv
Tcoupl  =  nose-hoover
tau_t   =  0.1 0.1 0.1
ref_t   =  295 295 295
tc_grps = CNT grp1 grp2
gen_temp= 295

Your answer to any of these questions would be a ton of help!
These potential energies are the average ones, how can I get the final
potential of the system? Are average potentials good terms to decide if the
simulation was wrong?


The .edr file contains energies at every nstenergy steps.  An instantaneous 
value is not terribly useful, though.



Can the positive potentials be the effect of forcefield inappropriate files?
The system is a CNT containing some solvent. Can positive potentials be the
reflection of the system's angle pressure not willing to reform from plane
graphene system?



The outcome indicates that the potential energy is dominated by bonded (i.e. 
intramolecular) interactions, while there are few/weak nonbonded interactions 
among the atoms in the system.  If I'm interpreting what you're saying, there is 
some solvent inside the CNT, and nothing outside?  Generally, most condensed 
phase systems (at least those in water) are dominated by electrostatic 
interactions, whereas your system has a negligible amount of electrostatics. 
The overall effect is a function of what your species are.  But for that, you're 
going to have to tell us what grp1 and grp2 are, what their topologies are, etc.


But in reality, there seems to be nothing wrong with the simulation; it's just 
atypical, and you can't really compare it to a normal simulation with a lot of 
water.


-Justin

--
==

Justin A. Lemkul, Ph.D.

Re: [gmx-users] potential energy

[mah maz]

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   -30.2625
(kJ/mol)
Proper Dih. 60199.3 23845.936106.894
(kJ/mol)
LJ-14   40461.9 411748.27   -227.144
(kJ/mol)
Coulomb-140  0  0  0
(kJ/mol)
LJ (SR)-10117.72.6118.855   -3.85515
(kJ/mol)
Coulomb (SR)   -156.169  9 40.82335.6671
(kJ/mol)
Potential118733 741142.65   -420.414
(kJ/mol)
Kinetic En. 14932.17.3423.825   -50.1192
(kJ/mol)
Total Energy 133665 811221.66   -470.533
(kJ/mol)
Conserved En.180812 57121.277397.186
(kJ/mol)
Temperature 295.064   0.148.37495  -0.990376  (K)
Pressure  -0.072961   0.17 17.163  -0.120159  (bar)
Vir-XX  4860.4521021707.326.9299
(kJ/mol)
Vir-XY  4.732333.3 1176.9   -2.74323
(kJ/mol)
Vir-XZ  3.180977.51907.36 4.2031
(kJ/mol)
Vir-YX  4.731473.31176.89   -2.74818
(kJ/mol)
Vir-YY  5388.86 39 5500.8202.824
(kJ/mol)
Vir-YZ0.05093923.21101.973.89409
(kJ/mol)
Vir-ZX  3.180897.51907.364.19967
(kJ/mol)
Vir-ZY0.05142363.21101.973.89442
(kJ/mol)
Vir-ZZ  4871.7620021686.431.3387
(kJ/mol)
Pres-XX0.156061   0.2525.1574  -0.125195  (bar)
Pres-XY  -0.00268517 0.00331.36879 0.00150158  (bar)
Pres-XZ  -0.00196111 0.00982.21263 -0.0154319  (bar)
Pres-YX  -0.00268417 0.00331.36879 0.00150732  (bar)
Pres-YY   -0.511872  0.0196.38934 -0.0849178  (bar)
Pres-YZ  0.000542369 0.00171.27895 0.00355122  (bar)
Pres-ZX  -0.00196102 0.00982.21263 -0.0154279  (bar)
Pres-ZY  0.000541808 0.00171.27895 0.00355084  (bar)
Pres-ZZ0.136928   0.2425.1334  -0.150365  (bar)
#Surf*SurfTen   8.815353.2359.945   -1.26863  (bar
nm)
T-CNT   295.063   0.148.44198  -0.997647  (K)
T-grp1  295.202   0.2138.5349   0.485478  (K)
T-grp2294.688   0.3253.7236   -2.39488  (K)



dt  =  0.0001
tinit   =  0
nsteps  =  200
nstxout =  1000
nstvout =  1000
nstfout =  0
nstlog  =  1000
nstenergy   =  1000
nstlist =  5
ns_type =  grid
rlist   =  0.9
coulombtype =  cutoff
rcoulomb= 0.9
rvdw=  0.9
pbc = xyz
integrator  = md-vv
Tcoupl  =  nose-hoover
tau_t   =  0.1 0.1 0.1
ref_t   =  295 295 295
tc_grps = CNT grp1 grp2
gen_temp= 295

Your answer to any of these questions would be a ton of help!
These potential energies are the average ones, how can I get the final
potential of the system? Are average potentials good terms to decide if the
simulation was wrong?
Can the positive potentials be the effect of forcefield inappropriate files?
The system is a CNT containing some solvent. Can positive potentials be the
reflection of the system's angle pressure not willing to reform from plane
graphene system?

I would appreciate your help. Many thanks in advance!
Regards,
Mah





On Sun, Jan 11, 2015 at 5:31 PM, mah maz mahma...@gmail.com 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
 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!
 Regards,
 Mah

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Re: [gmx-users] potential energy

[mah maz]

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!
Regards,
Mah
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Re: [gmx-users] potential energy

[Justin Lemkul]

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 term that isn't really relevant here when discussing the 
potential.  Many of the terms in the .edr contribute to the potential energy 
(because that's the definition of how force fields work), hence why I suggested 
that you look into them in more detail.


-Justin


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!
Regards,
Mah



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] potential energy

[Justin Lemkul]

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 are large and/or positive.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] potential energy

[Justin Lemkul]

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 of energy terms stored in an .edr 
file.  If you need further help, you're going to have to provide:


1. A full description of the system (what is it, how did you build it, etc)
2. Your full .mdp file
3. The full g_energy output (available options), copied and pasted from your 
terminal


-Justin


On Sun, Jan 11, 2015 at 12:52 AM, mah maz mahma...@gmail.com wrote:


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

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 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
stability of the system. In my simulation, potential energy is positive and
the total energy is a big positive number, but no explosion happened. What
is the problem?
thank you!








--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] potential energy

[mah maz]

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 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
 stability of the system. In my simulation, potential energy is positive and
 the total energy is a big positive number, but no explosion happened. What
 is the problem?
 thank you!

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Re: [gmx-users] potential energy

[mah maz]

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

 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 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
 stability of the system. In my simulation, potential energy is positive and
 the total energy is a big positive number, but no explosion happened. What
 is the problem?
 thank you!



-- 
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* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] potential energy

[Justin Lemkul]

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, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] potential energy

[Justin Lemkul]

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.  Various components are also printed out to the 
various energy terms printed by g_energy.



and its summation with the kinetic energy should be negative showing the
stability of the system. In my simulation, potential energy is positive and
the total energy is a big positive number, but no explosion happened. What
is the problem?


That depends entirely upon what your system is.  A negative potential is 
generally expected for most condensed-phase systems, in which attractive 
nonbonded interactions dominate over repulsive terms.  But the energy of a given 
system is entirely dependent upon what the system is.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] potential energy

[mah maz]

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 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

 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 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
 stability of the system. In my simulation, potential energy is positive and
 the total energy is a big positive number, but no explosion happened. What
 is the problem?
 thank you!




-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] potential energy

[Meenakshi Rajput]

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 ashi.rajpu...@gmail.com
  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.
  On Aug 11, 2014 2:32 PM, Meenakshi Rajput ashi.rajpu...@gmail.com
 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; Stop minimization when the energy changes
 by less than emtol kJ/mol.
 nsteps= 200; Maximum number of (minimization) steps to
 perform
 nstenergy= 10; Write energies to disk every nstenergy steps
 nstxtcout= 10; Write coordinates to disk every nstxtcout
 steps
 xtc_grps= Protein; Which coordinate group(s) to write to disk
 energygrps= Protein; Which energy group(s) to write to disk
 nstlist= 5; Frequency to update the neighbor list and
 long range forces
 ns_type= grid  ; Method to determine neighbor list (simple,
 grid)
 rlist= 1.2; Cut-off for making neighbor list (short
 range forces)
 coulombtype= PME   ; Treatment of long range electrostatic
 interactions
 rcoulomb= 1.2; long range electrostatic cut-off
 rvdw= 1.2; long range Van der Waals cut-off
 constraints= none; Bond types to replace by constraints
 pbc= xyz; Periodic Boundary Conditions (yes/no0
 After the run, potential energy is negative. can you tell me whats the
 problem??



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Re: [gmx-users] potential energy

[Meenakshi Rajput]

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 10:33 PM, Meenakshi Rajput ashi.rajpu...@gmail.com
wrote:

 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 
 ashi.rajpu...@gmail.com 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.
  On Aug 11, 2014 2:32 PM, Meenakshi Rajput ashi.rajpu...@gmail.com
 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; Stop minimization when the energy changes
 by less than emtol kJ/mol.
 nsteps= 200; Maximum number of (minimization) steps to
 perform
 nstenergy= 10; Write energies to disk every nstenergy steps
 nstxtcout= 10; Write coordinates to disk every nstxtcout
 steps
 xtc_grps= Protein; Which coordinate group(s) to write to disk
 energygrps= Protein; Which energy group(s) to write to disk
 nstlist= 5; Frequency to update the neighbor list and
 long range forces
 ns_type= grid  ; Method to determine neighbor list (simple,
 grid)
 rlist= 1.2; Cut-off for making neighbor list (short
 range forces)
 coulombtype= PME   ; Treatment of long range electrostatic
 interactions
 rcoulomb= 1.2; long range electrostatic cut-off
 rvdw= 1.2; long range Van der Waals cut-off
 constraints= none; Bond types to replace by constraints
 pbc= xyz; Periodic Boundary Conditions (yes/no0
 After the run, potential energy is negative. can you tell me whats the
 problem??



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Re: [gmx-users] potential energy

[Justin Lemkul]

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; Stop minimization when the energy changes by
less than emtol kJ/mol.
nsteps= 200; Maximum number of (minimization) steps to
perform
nstenergy= 10; Write energies to disk every nstenergy steps
nstxtcout= 10; Write coordinates to disk every nstxtcout steps
xtc_grps= Protein; Which coordinate group(s) to write to disk
energygrps= Protein; Which energy group(s) to write to disk
nstlist= 5; Frequency to update the neighbor list and long
range forces
ns_type= grid  ; Method to determine neighbor list (simple,
grid)
rlist= 1.2; Cut-off for making neighbor list (short range
forces)
coulombtype= PME   ; Treatment of long range electrostatic
interactions
rcoulomb= 1.2; long range electrostatic cut-off
rvdw= 1.2; long range Van der Waals cut-off
constraints= none; Bond types to replace by constraints
pbc= xyz; Periodic Boundary Conditions (yes/no0
After the run, potential energy is negative. can you tell me whats the
problem??



There is none.  The potential should be negative.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Gromacs Users mailing list

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Re: [gmx-users] potential energy

[Meenakshi Rajput]

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 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
 less than emtol kJ/mol.
 nsteps= 200; Maximum number of (minimization) steps to
 perform
 nstenergy= 10; Write energies to disk every nstenergy steps
 nstxtcout= 10; Write coordinates to disk every nstxtcout steps
 xtc_grps= Protein; Which coordinate group(s) to write to disk
 energygrps= Protein; Which energy group(s) to write to disk
 nstlist= 5; Frequency to update the neighbor list and long
 range forces
 ns_type= grid  ; Method to determine neighbor list (simple,
 grid)
 rlist= 1.2; Cut-off for making neighbor list (short range
 forces)
 coulombtype= PME   ; Treatment of long range electrostatic
 interactions
 rcoulomb= 1.2; long range electrostatic cut-off
 rvdw= 1.2; long range Van der Waals cut-off
 constraints= none; Bond types to replace by constraints
 pbc= xyz; Periodic Boundary Conditions (yes/no0
 After the run, potential energy is negative. can you tell me whats the
 problem??

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Re: [gmx-users] potential energy

[Justin Lemkul]

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 should always be negative (net 
attraction).  If the potential becomes positive (net repulsion), your system is 
probably very unstable.


If you're using CHARMM, then yes, your .mdp settings are incorrect.  You should 
be applying a force switch to the LJ terms over 1.0-1.2 nm and you should 
constraint h-bonds.


-Justin


On Aug 11, 2014 2:32 PM, Meenakshi Rajput ashi.rajpu...@gmail.com 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; Stop minimization when the energy changes by
less than emtol kJ/mol.
nsteps= 200; Maximum number of (minimization) steps to
perform
nstenergy= 10; Write energies to disk every nstenergy steps
nstxtcout= 10; Write coordinates to disk every nstxtcout steps
xtc_grps= Protein; Which coordinate group(s) to write to disk
energygrps= Protein; Which energy group(s) to write to disk
nstlist= 5; Frequency to update the neighbor list and long
range forces
ns_type= grid  ; Method to determine neighbor list (simple,
grid)
rlist= 1.2; Cut-off for making neighbor list (short range
forces)
coulombtype= PME   ; Treatment of long range electrostatic
interactions
rcoulomb= 1.2; long range electrostatic cut-off
rvdw= 1.2; long range Van der Waals cut-off
constraints= none; Bond types to replace by constraints
pbc= xyz; Periodic Boundary Conditions (yes/no0
After the run, potential energy is negative. can you tell me whats the
problem??



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] potential energy

[Meenakshi Rajput]

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 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 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
 less than emtol kJ/mol.
 nsteps= 200; Maximum number of (minimization) steps to
 perform
 nstenergy= 10; Write energies to disk every nstenergy steps
 nstxtcout= 10; Write coordinates to disk every nstxtcout
 steps
 xtc_grps= Protein; Which coordinate group(s) to write to disk
 energygrps= Protein; Which energy group(s) to write to disk
 nstlist= 5; Frequency to update the neighbor list and
 long range forces
 ns_type= grid  ; Method to determine neighbor list (simple,
 grid)
 rlist= 1.2; Cut-off for making neighbor list (short range
 forces)
 coulombtype= PME   ; Treatment of long range electrostatic
 interactions
 rcoulomb= 1.2; long range electrostatic cut-off
 rvdw= 1.2; long range Van der Waals cut-off
 constraints= none; Bond types to replace by constraints
 pbc= xyz; Periodic Boundary Conditions (yes/no0
 After the run, potential energy is negative. can you tell me whats the
 problem??


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Re: [gmx-users] Potential energy calculations

[Justin Lemkul]

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 it properly alighn the energy based on the averidged zero
point.  I ask, not knowing, but playing with this (single small molecules), I
found the systems standard error swamps the potential energy, and you then get a
proper shaped graph, where the axis has to be corrected by an energy term (is
what I meant by zeroing).  I did this with just h2o playing around out of
boardom at some point...as I had 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...


We're not dealing with a single molecule, at least assuming I understand what 
the OP is discussing.  One has a homogeneous box of solvent, such that the 
potential energy of the system can be divided evenly between equivalent 
molecules and averaged over time.  The literature often reports the 
configurational energy of such a liquid.


I'm not entirely sure what it is that you were playing around with, but such 
decompositions as these are not suited for heterogeneous systems, and what 
you've come up with really just sounds like a way of looking at the 
interconversion of kinetic and potential energy.


-Justin


Stephan
*Gesendet:* Donnerstag, 26. Dezember 2013 um 14:04 Uhr
*Von:* 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 a single
  simulation. Thus you have to find a beginning point and subtract it across 
the
  run. Additionally, fluctuations may dictate 10 or so runs to determine a good
  mean, as the drifet or error might be 20 kcal/mol in a system. As I read your
  other post, I would assume the experiment would be non random placement of 
DMSO
  in water (say a wall system), otherwise you would be looking at a single
  molecules energy dictated by conformational space over time...ie something 
like
  Justin's post...which you still may have to calculate a mean for, but I 
assume
  this is done through the -nmol option. You still also may have to zero it,
  but I am not sure, direct use of g_energy gives abitrary starting points as
  above from my experience.
 

The values printed by g_energy are not arbitrary. They are the energy of a mole
of equivalent systems of a given configuration, hence their large magnitude.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: [gmx-users] Potential energy

[Justin Lemkul]

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 not this means I must perform my
simulation again?



There is no .mdp option to calculate the potential energy of just a single 
group.  One can excluded nonbonded interactions between pairs of groups or 
decompose nonbonded energy between pairs of groups.


One could obtain the potential energy of a group by stripping out the 
coordinates of interest from the original trajectory (with trjconv), making a 
matching .tpr file (with tpbconv), then recalculating energies with mdrun 
-rerun.  Such a quantity would be useless, though.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Potential energy calculations

[lloyd riggs]

I got boared at one point and indexed everything, and was looking at total energy, but found if you look at any parameter (LJSR, etc...) for solvent they appear like sinusoidal...but was jsut in my brain equating these to potential energy, and assumed the OP was trying to look at only the DMSO not the system, thus trying to make a stab at it. Couldnt figure out how to deliniate the two, as the error estimates would overlap to the point of making either non-significant, without a perterbation, and you cant direct plot potential for an indexed molecule (summed other energies), but the potential for a whole simple system has a very large standard error and drift, which overlaps the small molecules potential energies, in any case, I let it rest now happy hollidays...



Sincerely,



Stephan Watkins


Gesendet:Samstag, 28. Dezember 2013 um 00:52 Uhr
Von:Justin Lemkul jalem...@vt.edu
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 it properly alighn the energy based on the averidged zero
 point. I ask, not knowing, but playing with this (single small molecules), I
 found the systems standard error swamps the potential energy, and you then get a
 proper shaped graph, where the axis has to be corrected by an energy term (is
 what I meant by zeroing). I did this with just h2o playing around out of
 boardom at some point...as I had 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...

Were not dealing with a single molecule, at least assuming I understand what
the OP is discussing. One has a homogeneous box of solvent, such that the
potential energy of the system can be divided evenly between equivalent
molecules and averaged over time. The literature often reports the
configurational energy of such a liquid.

Im not entirely sure what it is that you were playing around with, but such
decompositions as these are not suited for heterogeneous systems, and what
youve come up with really just sounds like a way of looking at the
interconversion of kinetic and potential energy.

-Justin

 Stephan
 *Gesendet:* Donnerstag, 26. Dezember 2013 um 14:04 Uhr
 *Von:* 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 a single
  simulation. Thus you have to find a beginning point and subtract it across the
  run. Additionally, fluctuations may dictate 10 or so runs to determine a good
  mean, as the drifet or error might be 20 kcal/mol in a system. As I read your
  other post, I would assume the experiment would be non random placement of DMSO
  in water (say a wall system), otherwise you would be looking at a single
  molecules energy dictated by conformational space over time...ie something like
  Justins post...which you still may have to calculate a mean for, but I assume
  this is done through the -nmol option. You still also may have to zero it,
  but I am not sure, direct use of g_energy gives abitrary starting points as
  above from my experience.
 

 The values printed by g_energy are not arbitrary. They are the energy of a mole
 of equivalent systems of a given configuration, hence their large magnitude.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu  (410) 706-7441

 ==
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
 mail to gmx-users-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu  (410) 706-7441

==
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Re: [gmx-users] Potential energy

[Ali Alizadeh]

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 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 again?


 --
 Sincerely

 Ali Alizadeh

 Justin wrote:

There is no .mdp option to calculate the potential energy of just a single
group.  One can excluded nonbonded interactions between pairs of groups or
decompose nonbonded energy between pairs of groups.

One could obtain the potential energy of a group by stripping out the
coordinates of interest from the original trajectory (with trjconv), making a
matching .tpr file (with tpbconv), then recalculating energies with mdrun
-rerun.  Such a quantity would be useless, though.



-- 
Sincerely

Ali Alizadeh
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Re: [gmx-users] Potential energy calculations

[lloyd riggs]

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 it properly alighn the energy based on the averidged zero point. I ask, not knowing, but playing with this (single small molecules), I found the systems standard error swamps the potential energy, and you then get a proper shaped graph, where the axis has to be corrected by an energy term (is what I meant by zeroing). I did this with just h2o playing around out of boardom at some point...as I had 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 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 a single
 simulation. Thus you have to find a beginning point and subtract it across the
 run. Additionally, fluctuations may dictate 10 or so runs to determine a good
 mean, as the drifet or error might be 20 kcal/mol in a system. As I read your
 other post, I would assume the experiment would be non random placement of DMSO
 in water (say a wall system), otherwise you would be looking at a single
 molecules energy dictated by conformational space over time...ie something like
 Justins post...which you still may have to calculate a mean for, but I assume
 this is done through the -nmol option. You still also may have to zero it,
 but I am not sure, direct use of g_energy gives abitrary starting points as
 above from my experience.


The values printed by g_energy are not arbitrary. They are the energy of a mole
of equivalent systems of a given configuration, hence their large magnitude.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu  (410) 706-7441

==
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Re: [gmx-users] Potential energy calculations

[virk]

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@

 gt; wrote:
 
 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 Nabble.com.
 --
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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to 

 gmx-users-request@

 .

 
 
 
 -- 
 
 ==
 
 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow
 
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalemkul@.umaryland

  | (410) 706-7441
 
 
 ==
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 Gromacs Users mailing list
 
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 a mail to 

 gmx-users-request@

 .


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@

 gt; wrote:
 
 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 Nabble.com.
 --
 Gromacs Users mailing list

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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

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 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to 

 gmx-users-request@

 .

 
 
 
 -- 
 
 ==
 
 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow
 
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalemkul@.umaryland

  | (410) 706-7441
 
 
 ==
 -- 
 Gromacs Users mailing list
 
 * Please search the archive at
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 a mail to 

 gmx-users-request@

 .


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@

 gt; wrote:
 
 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 Nabble.com.
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

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 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to 

 gmx-users-request@

 .

 
 
 
 -- 
 
 ==
 
 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow
 
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalemkul@.umaryland

  | (410) 706-7441
 
 
 ==
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 * For 

Re: [gmx-users] Potential energy calculations

[lloyd riggs]

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 Average Err.Est. RMSD Tot-Drift
---
Potential -28160.8 4 259.924 24.189
(kJ/mol)

But according to some papers average potential energy value is 49.1
(KJ/mol).

Everything else seems to match this paper (density, diffusion coefficient)
except potential energy.

Am I missing something over here or my system is wrong.

I would be very thankful for your help and time.

Amninder Virk




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Re: [gmx-users] Potential energy calculations

[Robert Darkins]

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 values of

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Potential  -28160.8  4259.924 24.189
(kJ/mol)

  But according to some papers average potential energy value is 49.1
(KJ/mol).

Everything else seems to match this paper (density, diffusion coefficient)
except potential energy.

Am I missing something over here or my system is wrong.

I would be very thankful for your help and time.

Amninder Virk




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Re: [gmx-users] Potential energy calculations

[virk]

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 

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Re: [gmx-users] Potential energy calculations

[virk]

I am trying to simulate mixture of DMSO and water at different mole
fractionbut this value is for 100% DMSO.

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