[gmx-users] All atom coordinates for Test Particle Insertion

[Badmos, Sakiru]

Hi everyone,

  I want to calculate excess chemical potential for some 
molecules in water. I found a tutorial on this but it was on methane (united 
atom). The insertion of the test particle requires that its included in the 
.gro file with coordinate 0.000 0.000 0.000. This works for United atom. How do 
I do this for molecule like CO2 with three atoms?

 Thank you as you help.

Sakiru.
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[gmx-users] wt% of the solvent

[Sam Dav]

Hello GROMACS users.
I'm trying to solvate a polymer in (20 wt% alcohol +80 wt% water)
which command should I use to get the correct percentage? I'm using linux.
or should I calculate the number of molecules in the box.
Thanks in advance
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Re: [gmx-users] Protein ligand complex simulation

[RAHUL SURESH]

I mean the ligand is not bonded with the protein.


On Sat, 1 Apr 2017 at 6:29 PM, RAHUL SURESH  wrote:

> I followed the complex simulation tutorial. Minimisation for 2ns
>
> I used auto dock to dock ligand with protein. During simulation I find the
> ligand out of protein. Is that usual?
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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[gmx-users] NPT file parameters

[Pranesh M]

Dear All,

I am trying to generate simulation for ionic liquid and aromatic compound.
No water molecule is involved in my system.
In the NPT.mdp file parameters, should I change the compressibility value
of my aromatic compound or ionic liquid?
; Pressure coupling  =
Pcoupl   = Parrinello-Rahman ; Extended-ensemble pressure
coupling, box vectors are subject to an equation of motion
Pcoupltype   = isotropic   ; same in xyz direction
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 1.0  ; time constant for coupling
compressibility  = 4.5e-5  ; For water at 1 atm and 300 K the
compressibility is 4.5e-5 [bar-1]
ref_p= 1.0   ; reference pressure for
coupling

Thanks.
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[gmx-users] Energy Miinimization question

[Mishelle Oña]

Hello everybody,

I have a question about the final conformation after energy minimization. I am 
simulating a polymer in vacuo and I used steepest descent method for energy 
minimization. When I use an emtol=1000 the structure I get is linear. Then I 
tried an emtol=30 because another study about the same polymer used this value 
but the final structure has some rings, I am not sure why this happened.

Thanks for your help.

Mishelle
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[gmx-users] Protein ligand complex simulation

[RAHUL SURESH]

I followed the complex simulation tutorial. Minimisation for 2ns

I used auto dock to dock ligand with protein. During simulation I find the
ligand out of protein. Is that usual?
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] HYDROGEN BOND EXISTENCE MAP

[Neha Gupta]

Thanks.

On Sat, Apr 1, 2017 at 12:59 PM, Sheeja Vasudevan 
wrote:

>
> Hi Neha,
>
> If I understand correctly pdb file is used for extracting information
> about the topology of the molecule..in this case the atom name and type.
> so it does not matter at which time point of time in your simulation your
> pdb file is generated as long as it is whole molecule.
>
> Best
> Sheeja.
>
> > Hi gromacs users,
> >
> > In the perl script to calculate hydrogen bond %, the command is
> >
> > perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx
> >
> >
> > What should the structure.pdb file contain?
> >
> > How to obtain it?
> >
> > At which point of simulations?
> >
> > Thanks,
> > Neha
> > --
> > Gromacs Users mailing list
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> >
>
>
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Re: [gmx-users] HYDROGEN BOND EXISTENCE MAP

[Sheeja Vasudevan]

Hi Neha,

If I understand correctly pdb file is used for extracting information
about the topology of the molecule..in this case the atom name and type.
so it does not matter at which time point of time in your simulation your
pdb file is generated as long as it is whole molecule.

Best
Sheeja.

> Hi gromacs users,
>
> In the perl script to calculate hydrogen bond %, the command is
>
> perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx
>
>
> What should the structure.pdb file contain?
>
> How to obtain it?
>
> At which point of simulations?
>
> Thanks,
> Neha
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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>


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Re: [gmx-users] INTERPRETING THE ENERGY VALUES AFTER SIMULATIONS IN GROMACS

[David van der Spoel]

On 01/04/17 06:42, Kulkarni R wrote:

Hi gromacs users,

After protein ligand simulations, I want to do energy analysis.

How to interpret the following data properly? What books and papers should we 
refer?

Energy   AverageErr.Est.   RMSDTot-Drift
---
Coul-SR:Protein-MOL-12.45493.611.7667   -19.8497  (kJ/mol)
LJ-SR:Protein-MOL-103.5021.17.06959 6.6227  (kJ/mol)

What is the significance of total drift?

Can someone offer suggestions and help me to improve?

Thanks,
Kulkarni.R

These numbers have no real physical meaning isolated from the rest of 
the system. Please check tutorials on free energy calculation.


--
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] Water models for Heterogeneous ice nucleation

[David van der Spoel]

On 01/04/17 08:15, Hana Ripperdá wrote:

Hi,
I want to study the ice nucleation by gromacs software. Are TIP4P/2005 and
SPC/E water models available for that? I mean, the water models are
suitable to study super cool water and  phase change?

Thank you in advance
Hana


How about TIP4P/Ice?

--
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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[gmx-users] Water models for Heterogeneous ice nucleation

[Hana Ripperdá]

Hi,
I want to study the ice nucleation by gromacs software. Are TIP4P/2005 and
SPC/E water models available for that? I mean, the water models are
suitable to study super cool water and  phase change?

Thank you in advance
Hana
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