Re: [gmx-users] Re: Coupling groups for nvt equilibration

[Justin A. Lemkul]

neeru sharma wrote:

Thanks Justin.

I have tried both ways now and considering Protein_MG_GDP and Water_ions 
groups, it is running without any error but Protein_GDP and 
MG_Water_ions is failing with an error message.




Well, without knowing the exact error message and all the steps you did 
preceding that to set up the index groups, there's nothing anyone can do to 
help, though I don't think it's necessary anyway.  You have a set of groups 
that's working and that makes sense for your system.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: Coupling groups for nvt equilibration

[neeru sharma]

Thanks Justin.

I have tried both ways now and considering Protein_MG_GDP and Water_ions
groups, it is running without any error but Protein_GDP and MG_Water_ions
is failing with an error message.

Thanks again...


Neeru

>
> neeru sharma wrote:
> >
> >
> > Thanks Justin.
> >
> > I tried the simulation with Protein_GDP and Water_ions, considering that
> > "Water_and_ions" group will include MG. But it didn't work showing an
> > error,saying "One atom not present in the coupling group". Shall I try
> > to include MG in Water_ions group via make_ndx ?
> >
>
> I think the better approach is the one you posted before.
>
> -Justin
>
> >
> > 
> > Neeru
> >
> > neeru sharma wrote:
> >  > Dear Gromacs users,
> >  >
> >  >
> >  > I am simulating a system containing a protein with covalently
> > attached
> >  > Mg in complex with GDP.
> >  >
> >  > For nvt equilibration, I have taken protein+Mg+GDP as the single
> > group
> >  > and Water+ions as the other. The corresponding block from the
> > .mdp file
> >  > is below:
> >  >
> >  > -- ; Temperature coupling is on
> >  > tcoupl  = V-rescale
> >  > tc-grps = Protein_MG_GDP Water_and_ions
> >  >
> >  >
> >  >
> >  > Is this coupling method correct, to treat Protein and Mg as
> different
> >  > quantities?
> >  >
> >
> > You are not treating them differently; they are in a merged group.
> >  Note,
> > though, that the default "Water_and_ions" group will include MG, and
> > thus grompp
> > with throw a fatal error.  You'll have to create a custom group for
> > this one, as
> > well.  Otherwise, the approach seems reasonable to me.
> >
> > -Justin
> >
> > --
> > 
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu  | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> >
>
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Re: [gmx-users] Re: Coupling groups for nvt equilibration

[Justin A. Lemkul]

neeru sharma wrote:



Thanks Justin.

I tried the simulation with Protein_GDP and Water_ions, considering that 
"Water_and_ions" group will include MG. But it didn't work showing an 
error,saying "One atom not present in the coupling group". Shall I try 
to include MG in Water_ions group via make_ndx ?




I think the better approach is the one you posted before.

-Justin




Neeru

neeru sharma wrote:
 > Dear Gromacs users,
 >
 >
 > I am simulating a system containing a protein with covalently
attached
 > Mg in complex with GDP.
 >
 > For nvt equilibration, I have taken protein+Mg+GDP as the single
group
 > and Water+ions as the other. The corresponding block from the
.mdp file
 > is below:
 >
 > -- ; Temperature coupling is on
 > tcoupl  = V-rescale
 > tc-grps = Protein_MG_GDP Water_and_ions
 >
 >
 >
 > Is this coupling method correct, to treat Protein and Mg as different
 > quantities?
 >

You are not treating them differently; they are in a merged group.
 Note,
though, that the default "Water_and_ions" group will include MG, and
thus grompp
with throw a fatal error.  You'll have to create a custom group for
this one, as
well.  Otherwise, the approach seems reasonable to me.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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[gmx-users] Re: Coupling groups for nvt equilibration

[neeru sharma]

Thanks Justin.

I tried the simulation with Protein_GDP and Water_ions, considering that
"Water_and_ions" group will include MG. But it didn't work showing an
error,saying "One atom not present in the coupling group". Shall I try to
include MG in Water_ions group via make_ndx ?



Neeru

neeru sharma wrote:
> > Dear Gromacs users,
> >
> >
> > I am simulating a system containing a protein with covalently attached
> > Mg in complex with GDP.
> >
> > For nvt equilibration, I have taken protein+Mg+GDP as the single group
> > and Water+ions as the other. The corresponding block from the .mdp file
> > is below:
> >
> > -- ; Temperature coupling is on
> > tcoupl  = V-rescale
> > tc-grps = Protein_MG_GDP Water_and_ions
> >
> >
> >
> > Is this coupling method correct, to treat Protein and Mg as different
> > quantities?
> >
>
> You are not treating them differently; they are in a merged group.  Note,
> though, that the default "Water_and_ions" group will include MG, and thus
> grompp
> with throw a fatal error.  You'll have to create a custom group for this
> one, as
> well.  Otherwise, the approach seems reasonable to me.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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