[gmx-users] Problem in calculating static dielectric constant of Lysozymes

[Suman Das]

Dear Gromacs Users,

I am trying to calculate static dielectric constant of Lysozymes using
gromacs version 4.6.7. I tried to follow the protocol used earlier by van
Gunsteren (J. Phys. Chem. 1993, 97, 2009-2014).  I used PME for the
electrostatic interaction. First, I converted the trajectory of protein by
using the command 'trjconv -f traj.xtc -o protein.xtc -pbc whole -e
1000.0". Then I removed the translational and rotational motion of the
protein w.r.t the C-alpha atom by the following command "trjconv -f
protein.xtc -o protein_fit.xtc -fit rot+trans". I choose C-alpha for the
least square fit. And finally g_dipoles command to calculate the dielectric
constant "g_dipoles -f protein_fit.xtc -o Mtot.xvg -eps epsilon.xvg -a
aver.xvg -d dipdist.xvg -c dipcorr.xvg". However, the dielectric constant
value (1.04) that I am getting is very less compared to the actual
dielectric constant (30).


Dipole moment (Debye)
-
Average  = 172.7138  Std. Dev. =   7.4113  Error =   0.0524

The following averages for the complete trajectory have been calculated:

 Total < M_x > = 38.9789 Debye
 Total < M_y > = 54.2911 Debye
 Total < M_z > = -158.896 Debye

 Total < M_x^2 > = 1575.16 Debye^2
 Total < M_y^2 > = 3006.62 Debye^2
 Total < M_z^2 > = 25303.2 Debye^2

 Total < |M|^2 > = 29885 Debye^2
 Total |< M >|^2 = 29714.9 Debye^2

 < |M|^2 > - |< M >|^2 = 170.091 Debye^2

Finite system Kirkwood g factor G_k = 0.00570201
Infinite system Kirkwood g factor g_k = 0.00561463

Epsilon = 1.04819

Could you help me to find out what probably went wrong with the calculation?

Thanks,
Suman
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Re: [gmx-users] zero value for non-Protein components in energygrps

[Mark Abraham]

Hi,

Note that the easiest way to do that is gmx mdrun -nb cpu -rerun your.trr.
Your original log file did warn you about the zero energies.

Mark

On Tue, Oct 31, 2017 at 8:11 PM Mohammad Hassan Khatami 
wrote:

> Thanks Justin!
>
> That was the issue.
>
> MHK
>
>
> On 2017-10-31 01:35 PM, Justin Lemkul wrote:
> >
> >
> > On 10/31/17 12:07 PM, Mohammad Hassan Khatami wrote:
> >> Hi,
> >>
> >> I have an issue with calculating energy groups in GMX2016.4, while
> >> running a simple protein in water tutorial using the default oplsAA
> >> forcefield in gromacs. I searched my problem it in the mailing list
> >> but did not find my answer.
> >>
> >> In addition to the default tutorial results, I wanted to print out
> >> the energy values for different components of the simulation, i.e.,
> >> protein and water, in the .edr file. So I added the line below to the
> >> .mdp file to calculate values for different energy groups:
> >>
> >>
> >> energygrps = Protein SOL
> >>
> >> After running a short simulation, I calculated the different energy
> >> values and the output is as follow:
> >>
> >> Energy  Average   Err.Est.   RMSD Tot-Drift
> >>
> ---
> >>
> >> LJ-14   3004.955.3 54.675
> >> 44.9933  (kJ/mol)
> >> Coulomb-14 7927.054.144.0138 -4.19923
> >> (kJ/mol)
> >> LJ (SR) 21978.8110500.505
> >> 752.675  (kJ/mol)
> >> Coulomb (SR)   -2083842201438.51 -1321.11
> >> (kJ/mol)
> >> Coul-SR:Protein-Protein -2083842201438.51   -1321.11
> >> (kJ/mol)
> >> LJ-SR:Protein-Protein  21978.8110500.505 752.675
> >> (kJ/mol)
> >> Coul-14:Protein-Protein   7927.054.144.0138 -4.19923
> >> (kJ/mol)
> >> LJ-14:Protein-Protein   3004.955.3 54.675 44.9933
> >> (kJ/mol)
> >> Coul-SR:Protein-SOL   0  0  0
> >> 0(kJ/mol)
> >> LJ-SR:Protein-SOL   0  0 0  0
> >> (kJ/mol)
> >> Coul-14:Protein-SOL   0  0  0 0
> >> (kJ/mol)
> >> LJ-14:Protein-SOL   0  0 0  0
> >>  (kJ/mol)
> >> Coul-SR:SOL-SOL0  0 0  0
> >> (kJ/mol)
> >> LJ-SR:SOL-SOL0  0 0  0
> >>(kJ/mol)
> >> Coul-14:SOL-SOL0  0 0  0
> >> (kJ/mol)
> >> LJ-14:SOL-SOL0  0 0 0
> >> (kJ/mol)
> >>
> >> Here, all the energy values for the Protein-SOL and SOL-SOL are zero,
> >> which is not what I expected. Moreover, the general LJ-14,
> >> Coulomb-14, LJ (SR) and Coulomb (SR) are exactly the values
> >> calculated for only protein.
> >>
> >> When I run them individually, i.e., only water system and only
> >> protein system, I get non-zero values, which are expected.
> >>
> >> Is there any other flag except  "energygrps" that I forgot to
> >> implement in my mdp file? and why is it only calculating the values
> >> of the protein  in the general LJ-14, Coulomb-14, LJ (SR) and Coulomb
> >> (SR) energies.
> >>
> >
> > If you did the simulation on GPU, energygrps are not supported. Do an
> > mdrun -rerun on the trajectory using just CPU hardware to obtain these
> > energies.
> >
> > -Justin
> >
>
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Re: [gmx-users] zero value for non-Protein components in energygrps

[Mohammad Hassan Khatami]

Thanks Justin!

That was the issue.

MHK


On 2017-10-31 01:35 PM, Justin Lemkul wrote:



On 10/31/17 12:07 PM, Mohammad Hassan Khatami wrote:

Hi,

I have an issue with calculating energy groups in GMX2016.4, while 
running a simple protein in water tutorial using the default oplsAA 
forcefield in gromacs. I searched my problem it in the mailing list 
but did not find my answer.


In addition to the default tutorial results, I wanted to print out 
the energy values for different components of the simulation, i.e., 
protein and water, in the .edr file. So I added the line below to the 
.mdp file to calculate values for different energy groups:



energygrps = Protein SOL

After running a short simulation, I calculated the different energy 
values and the output is as follow:


Energy  Average   Err.Est.   RMSD Tot-Drift
--- 

LJ-14       3004.95    5.3 54.675 
44.9933  (kJ/mol)
Coulomb-14 7927.05    4.1    44.0138 -4.19923 
(kJ/mol)
LJ (SR)     21978.8    110    500.505 
752.675  (kJ/mol)
Coulomb (SR)       -208384    220    1438.51 -1321.11 
(kJ/mol)
Coul-SR:Protein-Protein -208384    220    1438.51   -1321.11 
(kJ/mol)
LJ-SR:Protein-Protein  21978.8    110    500.505 752.675 
(kJ/mol)
Coul-14:Protein-Protein   7927.05    4.1    44.0138 -4.19923 
(kJ/mol)
LJ-14:Protein-Protein   3004.95    5.3 54.675 44.9933 
(kJ/mol)
Coul-SR:Protein-SOL   0  0  0 
0    (kJ/mol)
LJ-SR:Protein-SOL       0  0 0  0         
    (kJ/mol)
Coul-14:Protein-SOL   0  0  0 0        
(kJ/mol)
LJ-14:Protein-SOL       0  0 0  0         
 (kJ/mol)
Coul-SR:SOL-SOL        0  0 0  0        
(kJ/mol)
LJ-SR:SOL-SOL    0  0 0  0     
           (kJ/mol)
Coul-14:SOL-SOL    0  0 0  0        
(kJ/mol)
LJ-14:SOL-SOL    0  0 0 0 
(kJ/mol)


Here, all the energy values for the Protein-SOL and SOL-SOL are zero, 
which is not what I expected. Moreover, the general LJ-14, 
Coulomb-14, LJ (SR) and Coulomb (SR) are exactly the values 
calculated for only protein.


When I run them individually, i.e., only water system and only 
protein system, I get non-zero values, which are expected.


Is there any other flag except  "energygrps" that I forgot to 
implement in my mdp file? and why is it only calculating the values 
of the protein  in the general LJ-14, Coulomb-14, LJ (SR) and Coulomb 
(SR) energies.




If you did the simulation on GPU, energygrps are not supported. Do an 
mdrun -rerun on the trajectory using just CPU hardware to obtain these 
energies.


-Justin



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Re: [gmx-users] zero value for non-Protein components in energygrps

[Justin Lemkul]

On 10/31/17 12:07 PM, Mohammad Hassan Khatami wrote:

Hi,

I have an issue with calculating energy groups in GMX2016.4, while 
running a simple protein in water tutorial using the default oplsAA 
forcefield in gromacs. I searched my problem it in the mailing list 
but did not find my answer.


In addition to the default tutorial results, I wanted to print out the 
energy values for different components of the simulation, i.e., 
protein and water, in the .edr file. So I added the line below to the 
.mdp file to calculate values for different energy groups:



energygrps = Protein SOL

After running a short simulation, I calculated the different energy 
values and the output is as follow:


Energy  Average   Err.Est.   RMSD Tot-Drift
--- 

LJ-14       3004.95    5.3 54.675 44.9933  
(kJ/mol)
Coulomb-14 7927.05    4.1    44.0138 -4.19923 
(kJ/mol)
LJ (SR)     21978.8    110    500.505 752.675  
(kJ/mol)
Coulomb (SR)       -208384    220    1438.51 -1321.11 
(kJ/mol)

Coul-SR:Protein-Protein -208384    220    1438.51   -1321.11 (kJ/mol)
LJ-SR:Protein-Protein  21978.8    110    500.505 752.675 (kJ/mol)
Coul-14:Protein-Protein   7927.05    4.1    44.0138 -4.19923 (kJ/mol)
LJ-14:Protein-Protein   3004.95    5.3 54.675 44.9933 
(kJ/mol)
Coul-SR:Protein-SOL   0  0  0 
0    (kJ/mol)
LJ-SR:Protein-SOL       0  0 0  0         
    (kJ/mol)
Coul-14:Protein-SOL   0  0  0 0            
(kJ/mol)
LJ-14:Protein-SOL       0  0 0  0         
 (kJ/mol)
Coul-SR:SOL-SOL        0  0 0  0         
   (kJ/mol)
LJ-SR:SOL-SOL    0  0 0  0         
       (kJ/mol)
Coul-14:SOL-SOL    0  0 0  0         
   (kJ/mol)
LJ-14:SOL-SOL    0  0 0 0 
(kJ/mol)


Here, all the energy values for the Protein-SOL and SOL-SOL are zero, 
which is not what I expected. Moreover, the general LJ-14, Coulomb-14, 
LJ (SR) and Coulomb (SR) are exactly the values calculated for only 
protein.


When I run them individually, i.e., only water system and only protein 
system, I get non-zero values, which are expected.


Is there any other flag except  "energygrps" that I forgot to 
implement in my mdp file? and why is it only calculating the values of 
the protein  in the general LJ-14, Coulomb-14, LJ (SR) and Coulomb 
(SR) energies.




If you did the simulation on GPU, energygrps are not supported. Do an 
mdrun -rerun on the trajectory using just CPU hardware to obtain these 
energies.


-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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[gmx-users] zero value for non-Protein components in energygrps

[Mohammad Hassan Khatami]

Hi,

I have an issue with calculating energy groups in GMX2016.4, while 
running a simple protein in water tutorial using the default oplsAA 
forcefield in gromacs. I searched my problem it in the mailing list but 
did not find my answer.


In addition to the default tutorial results, I wanted to print out the 
energy values for different components of the simulation, i.e., protein 
and water, in the .edr file. So I added the line below to the .mdp file 
to calculate values for different energy groups:



energygrps = Protein SOL

After running a short simulation, I calculated the different energy 
values and the output is as follow:


Energy  Average   Err.Est.   RMSD Tot-Drift
---
LJ-14       3004.95    5.3 54.675 44.9933  
(kJ/mol)

Coulomb-14 7927.05    4.1    44.0138 -4.19923  (kJ/mol)
LJ (SR)     21978.8    110    500.505 752.675  
(kJ/mol)

Coulomb (SR)       -208384    220    1438.51 -1321.11  (kJ/mol)
Coul-SR:Protein-Protein -208384    220    1438.51   -1321.11 (kJ/mol)
LJ-SR:Protein-Protein  21978.8    110    500.505 752.675  (kJ/mol)
Coul-14:Protein-Protein   7927.05    4.1    44.0138 -4.19923  (kJ/mol)
LJ-14:Protein-Protein   3004.95    5.3 54.675 44.9933  (kJ/mol)
Coul-SR:Protein-SOL   0  0  0 
0    (kJ/mol)
LJ-SR:Protein-SOL       0  0 0  0            
    (kJ/mol)
Coul-14:Protein-SOL   0  0  0 0              
   (kJ/mol)
LJ-14:Protein-SOL       0  0 0  0            
 (kJ/mol)
Coul-SR:SOL-SOL        0  0 0  0          
       (kJ/mol)
LJ-SR:SOL-SOL    0  0 0  0          
       (kJ/mol)
Coul-14:SOL-SOL    0  0 0  0          
       (kJ/mol)
LJ-14:SOL-SOL    0  0 0  
0 (kJ/mol)


Here, all the energy values for the Protein-SOL and SOL-SOL are zero, 
which is not what I expected. Moreover, the general LJ-14, Coulomb-14, 
LJ (SR) and Coulomb (SR) are exactly the values calculated for only protein.


When I run them individually, i.e., only water system and only protein 
system, I get non-zero values, which are expected.


Is there any other flag except  "energygrps" that I forgot to implement 
in my mdp file? and why is it only calculating the values of the 
protein  in the general LJ-14, Coulomb-14, LJ (SR) and Coulomb (SR) 
energies.


Best,

MHK


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Re: [gmx-users] Number of coordinates in .gro file does not match topology

[Ali Ahmed]

Hi,

Check your box size,I had a same problem. I used a larger box then the
problem solved.

Best
Ali

On Mon, Oct 30, 2017 at 6:29 PM, Mark Abraham 
wrote:

> Hi,
>
> How big is the system before and after? Gro format used fixed columns, so
> can sometimes struggle with large systems. Try using .g96 as the output
> file extension
>
> Mark
>
> On Mon, 30 Oct 2017 17:29  wrote:
>
> > Checked the file again. It is the one that gets generated after the
> > solvation command is run.
> >
> > Sent from my iPhone
> >
> > > On 30-Oct-2017, at 9:39 PM, Mark Abraham 
> > wrote:
> > >
> > > Hi,
> > >
> > > The most likely scenario is that you are looking at a gro file that is
> > not
> > > the one that was written by the solvation tool.
> > >
> > > Mark
> > >
> > > On Mon, Oct 30, 2017 at 9:41 AM Aishwarya Smriti <
> > > smritiaishwary...@gmail.com> wrote:
> > >
> > >> Hi!
> > >>
> > >> I'm trying to solvate a system of a CNT and a protein molecule. My
> > updated
> > >> topology file shows 106275 new solvent molecules added but the .gro
> file
> > >> has only coordinates for 6197 new molecules. I'm using SPC model for
> > >> solvating, Please help.
> > >>
> > >> Regards,
> > >> Aishwarya Smriti
> > >> Senior Undergraduate
> > >> Chemical Engineering
> > >> Indian Institute of Technology, Delhi
> > >> --
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> > >>
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Re: [gmx-users] Regarding water orientation profile

[João Henriques]

​Hi,

I've had similar issues in the past with the calculation of angular
distribution functions of water in respect to a given point or amino acid
residue and it wasn't easy/possible to solve with standard gromacs tools.
I'd suggest using MDAnalysis or some other equivalent tool. It definitely
gives you more freedom at the cost of having to code it yourself, plus it
can potentially be slow unless your Python skills are up to the challenge.
Here are a few examples you can use for "inspiration":

https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/waterdynamics.html

In any case, this is probably the least painful solution, since others
would revolve around wrapping one or more gromacs tools with some nasty
scripts, or coding a proper tool in C++ either from scratch or by building
on top of functions already available in gromacs source code.

Hope this helps,
Cheers,
J​

On Tue, Oct 31, 2017 at 8:55 AM, Dilip H N 
wrote:

> Hello,
> I want to do the water orientation profile for the amino-acid which is
> surrounded by water molecules as in my case amino-acid+water mixture.
> ie., i want to find out whether the water is orientation is more towards
> the N-terminal or towards the C-terminal of the amino acid and hence the
> orientation profile. I want to know throught the simulation around which
> terminal water molecules are more oriented as a function of time or etc.,
>
> I have a simulation done in GROMACS with one amino-acid in presence
> of cosolvents which is solvated with water for 10 ns. So I want to have the
> water orientation profile.But i tried with gmx sorient command, but i am
> unable to understand it.. and also through gmx h2order which
> calculates the orientation
> of water molecules with respect to the normal of the box, but i need to
> calculate with respect to N-terminal or through C-terminal.
> What is the best way to solve this..??
>
> Any suggestions are highly appreciated.
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
> ‌
>  Sent with Mailtrack
>  ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_
> medium=signature_campaign=signaturevirality>
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Re: [gmx-users] How good to use triclinic box for gormacs simulations?

[João Henriques]

Hi,

How does the link to "editconf" help in answering the original question?

Anyway, no, there is no specific recipe to select a box type. You generally
have to make an educated guess by using your scientific intuition and
knowledge about the shape (and conformational plasticity) of your system.
Then as the simulation runs, you keep checking the system's integrity to
see if it holds (is it interacting with its image?, etc). No box is
inherently inferior to another, it all depends on your system and how much
computational effort a particular box shape will save you (without
compromising the simulation).

Cheers,
J

On Tue, Oct 31, 2017 at 7:39 AM, Kunal Dutta <
kunal_lif...@mail.vidyasagar.ac.in> wrote:

> Hi,
> Please check the link.
> http://manual.gromacs.org/programs/gmx-editconf.html
> Best, Kunal
>
>
> On Tue, Oct 31, 2017 at 3:22 AM, vijayakumar gosu <
> vijayakumarg...@gmail.com
> > wrote:
>
> > Hello all,
> >
> >
> > I have performed simulations for Protein RNA complex around 1500
> residues.
> > I have used triclinic box with 1.4 nm distance from the edge of the box
> to
> > protein as triclinic box takes less number of water molecules (~10)
> > compared to other boxes . The simulation results looks fine and i am able
> > to answer the biological question. however i have not seen many
> > publications using triclinic box. Hence i am bit skeptical and like to
> > know  there is any criteria to choose the simulation box.
> >
> >
> > Thanks
> > --
> > 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.
> >
>
>
>
> --
> -
> Regards.
> Kunal Dutta
> Senior Research Scholar
> Microbiology and Immunology Laboratory
> Department of Human Physiology with Community Health
> Vidyasagar University, Medinipur-721102
> West Bengal, India.
> Cell: 9126181933
> 
> ORCID ID: -0002-0818-8787
> RG: https://www.researchgate.net/profile/Kunal_Dutta2
> GS: https://scholar.google.co.in/citations?user=ULby284J=en
>
> --
>
>
>
> 
> 
>
> *CONFIDENTIALITY NOTICE*
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[gmx-users] Regarding water orientation profile

[Dilip H N]

Hello,
I want to do the water orientation profile for the amino-acid which is
surrounded by water molecules as in my case amino-acid+water mixture.
ie., i want to find out whether the water is orientation is more towards
the N-terminal or towards the C-terminal of the amino acid and hence the
orientation profile. I want to know throught the simulation around which
terminal water molecules are more oriented as a function of time or etc.,

I have a simulation done in GROMACS with one amino-acid in presence
of cosolvents which is solvated with water for 10 ns. So I want to have the
water orientation profile.But i tried with gmx sorient command, but i am
unable to understand it.. and also through gmx h2order which
calculates the orientation
of water molecules with respect to the normal of the box, but i need to
calculate with respect to N-terminal or through C-terminal.
What is the best way to solve this..??

Any suggestions are highly appreciated.

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



‌
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Re: [gmx-users] How good to use triclinic box for gormacs simulations?

[Kunal Dutta]

Hi,
Please check the link.
http://manual.gromacs.org/programs/gmx-editconf.html
Best, Kunal


On Tue, Oct 31, 2017 at 3:22 AM, vijayakumar gosu  wrote:

> Hello all,
>
>
> I have performed simulations for Protein RNA complex around 1500 residues.
> I have used triclinic box with 1.4 nm distance from the edge of the box to
> protein as triclinic box takes less number of water molecules (~10)
> compared to other boxes . The simulation results looks fine and i am able
> to answer the biological question. however i have not seen many
> publications using triclinic box. Hence i am bit skeptical and like to
> know  there is any criteria to choose the simulation box.
>
>
> Thanks
> --
> 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.
>



-- 
-
Regards.
Kunal Dutta
Senior Research Scholar
Microbiology and Immunology Laboratory
Department of Human Physiology with Community Health
Vidyasagar University, Medinipur-721102
West Bengal, India.
Cell: 9126181933

ORCID ID: -0002-0818-8787
RG: https://www.researchgate.net/profile/Kunal_Dutta2
GS: https://scholar.google.co.in/citations?user=ULby284J=en

-- 





*CONFIDENTIALITY NOTICE*
This communication (including any attachment/s) is intended only for the 
use of the addressee(s) and contains information that is PRIVILEGED AND 
CONFIDENTIAL. Unauthorized reading, dissemination, distribution, or copying 
of this communication is prohibited.

*DISCLAIMER*
Any views or opinions presented in this email are solely those of the 
author and do not necessarily represent those the University.

WARNING:-
This communication, including any attachments, may not be free of viruses, 
interceptions or interference, and may not be compatible with your systems. 
You should carry out your own virus checks before opening any attachment to 
this e-mail. The sender of this e-mail and Vidyasagar University shall not 
be liable for any damage that you may sustain as a result of viruses, 
incompleteness of this message, a delay in receipt of this message or 
computer problems experienced.
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