Re: [gmx-users] couple-moltype in FREE ENERGY calculation

[Justin Lemkul]

On 2/20/20 11:36 AM, hind ahmed wrote:

Dear All,
I want to calculate the free energy of two different types of molecules in the 
same system. Is there a way to do this in gromacs?
couple-moltype   = CHOL  DPPC
Did not find any molecules of type 'CHOL DPPC' for coupling,


You can only decouple one [moleculetype] at a time. If you have a 
DPPC:CHOL bilayer, you shouldn't be attempting this because all you're 
going to do is cause the entire bilayer to disapper. Even if it's part 
of a larger mixture, you'll probably have a very hard time getting the 
simulations to converge.


-Justin

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[gmx-users] couple-moltype in FREE ENERGY calculation

[hind ahmed]

Dear All,
I want to calculate the free energy of two different types of molecules in the 
same system. Is there a way to do this in gromacs?
couple-moltype   = CHOL  DPPC
Did not find any molecules of type 'CHOL DPPC' for coupling,

Regards,
Hind
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Re: [gmx-users] couple-moltype

[Mark Abraham]

Hi,

You can only specify one moleculetype, but that entity can have more than
one molecule in it. So, make a salt pair moleculetype with at atoms section
that has the two ions you want, and make sure their coordinates are in
adjacent atom entries in the coordinate file in the right order for the
moleculetypes in your system in the usual way.

On Sat, Dec 9, 2017, 8:00 AM Jo  wrote:

> Hello,
>
> I would like to use the 'free-energy' function in gromacs to perform the
> gradual insertion method to calculate chemical potential.  In doing so, I
> would like to use 'couple-moltype' to specify the molecule type of the
> molecule that I inserting.  However, I am inserting 2 molecule types (Na
> and Cl, defined as 2 molecule types).  Is there a way that I can tell
> gromacs to include both molecules insertions in the free energy
> calculation?  In the documentation, I could only find how to specify 1
> molecule for the calculation.
>
> Thank you,
>
> Jo
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[gmx-users] couple-moltype

[Jo]

Hello,

I would like to use the 'free-energy' function in gromacs to perform the
gradual insertion method to calculate chemical potential.  In doing so, I
would like to use 'couple-moltype' to specify the molecule type of the
molecule that I inserting.  However, I am inserting 2 molecule types (Na
and Cl, defined as 2 molecule types).  Is there a way that I can tell
gromacs to include both molecules insertions in the free energy
calculation?  In the documentation, I could only find how to specify 1
molecule for the calculation.

Thank you,

Jo
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Re: [gmx-users] couple-moltype in FEP

[Hannes Loeffler]

On Tue, 12 Jul 2016 12:44:10 +0200
Alexander Alexander  wrote:

> Yes, Fig.6 comes from the different step in Fig.1. I think the
> easiest way here is to have 6 different "topol-mdp" files
> corresponding to each step. Although unlike the amino acid, defining
> the [ moleculetype ] for ion and a limited number of water molecules
> out of thousand of water molecules in the box would not be that easy.

I think it should be fairly straightforward to define two new
moleculetyps with a new name each, rename and reorder the coordinate
file accordingly and make the few changes in the [molecules] section.


> The harmonic restrants have been applied in step 1 and 3, can you
> please let me know what is the difference between them and also how I
> can apply each of them in md files?

You would need to read the paper.  Since this is a decoupling exercise
my guess would be that the restraints are relative to the Ti surface.
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Re: [gmx-users] couple-moltype in FEP

[Alexander Alexander]

Yes, Fig.6 comes from the different step in Fig.1. I think the easiest way
here is to have 6 different "topol-mdp" files corresponding to each step.
Although unlike the amino acid, defining the [ moleculetype ] for ion and a
limited number of water molecules out of thousand of water molecules in the
box would not be that easy.

The harmonic restrants have been applied in step 1 and 3, can you please
let me know what is the difference between them and also how I can apply
each of them in md files?

Thanks,
Regards,
Alex

On Tue, Jul 12, 2016 at 11:33 AM, Hannes Loeffler <
hannes.loeff...@stfc.ac.uk> wrote:

> On Tue, 12 Jul 2016 10:29:04 +0100
> Hannes Loeffler  wrote:
>
> > On Tue, 12 Jul 2016 10:16:24 +0200
> > Alexander Alexander  wrote:
> >
> > > Hi,
> > > Thanks for your response.
> > > I want to calculate the binding free energy of a single amino acid
> > > to a solid surface in aqueous solution by FEP, alchemical
> > > transformation, where perturbations applying on different species in
> > > ordered steps. For instance: Step.1 applying harmonic restraints  to
> > > the O and H of the amino acid. Step 2. Charges removal from the
> > > amino acid and two water molecules and an Ion, happen.
> >
> > I think the key figure here is actually Fig. 1.  What that paper
> > attempts to do is to replace a molecule on a surface with two water
> > molecules through a decoupling scheme.  I guess with Gromacs you would
> > have to manipulate the topology files to some extent because the
> > decharging and recharging steps involve different species (the sodium
> > ion is there only to offset any changes in total charge).
> > couple-lamnda0/1 may be helpful for some steps.  There are also both
> > insertions and deletions so I think step 3 must be split into two vdW
> > (deletion) steps.
>
> Thinking about step 3 you could probably also do it as a relative
> transformation i.e. omit couple-moltype and work with explicit A and B
> columns.
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Re: [gmx-users] couple-moltype in FEP

[Hannes Loeffler]

On Tue, 12 Jul 2016 10:29:04 +0100
Hannes Loeffler  wrote:

> On Tue, 12 Jul 2016 10:16:24 +0200
> Alexander Alexander  wrote:
> 
> > Hi,
> > Thanks for your response.
> > I want to calculate the binding free energy of a single amino acid
> > to a solid surface in aqueous solution by FEP, alchemical
> > transformation, where perturbations applying on different species in
> > ordered steps. For instance: Step.1 applying harmonic restraints  to
> > the O and H of the amino acid. Step 2. Charges removal from the
> > amino acid and two water molecules and an Ion, happen.
> 
> I think the key figure here is actually Fig. 1.  What that paper
> attempts to do is to replace a molecule on a surface with two water
> molecules through a decoupling scheme.  I guess with Gromacs you would
> have to manipulate the topology files to some extent because the
> decharging and recharging steps involve different species (the sodium
> ion is there only to offset any changes in total charge).
> couple-lamnda0/1 may be helpful for some steps.  There are also both
> insertions and deletions so I think step 3 must be split into two vdW
> (deletion) steps.

Thinking about step 3 you could probably also do it as a relative
transformation i.e. omit couple-moltype and work with explicit A and B
columns.
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Re: [gmx-users] couple-moltype in FEP

[Hannes Loeffler]

On Tue, 12 Jul 2016 10:16:24 +0200
Alexander Alexander  wrote:

> Hi,
> Thanks for your response.
> I want to calculate the binding free energy of a single amino acid to
> a solid surface in aqueous solution by FEP, alchemical
> transformation, where perturbations applying on different species in
> ordered steps. For instance: Step.1 applying harmonic restraints  to
> the O and H of the amino acid. Step 2. Charges removal from the amino
> acid and two water molecules and an Ion, happen.

I think the key figure here is actually Fig. 1.  What that paper
attempts to do is to replace a molecule on a surface with two water
molecules through a decoupling scheme.  I guess with Gromacs you would
have to manipulate the topology files to some extent because the
decharging and recharging steps involve different species (the sodium
ion is there only to offset any changes in total charge).
couple-lamnda0/1 may be helpful for some steps.  There are also both
insertions and deletions so I think step 3 must be split into two vdW
(deletion) steps.  Probably best to work this out by going through
steps 1 to 6 an pay careful attention to what species have zeroed out
charges.

It's unclear to me why you need to append any data.  What coordinates
you use doesn't really matter because each run is independent from
every other run (unless you see a specific need to take over a
coordinate from an adjacent lambda).
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Re: [gmx-users] couple-moltype in FEP

[Hannes Loeffler]

On Tue, 12 Jul 2016 07:35:00 +0100
Hannes Loeffler  wrote:

> On Tue, 12 Jul 2016 01:56:42 +0200
> Alexander Alexander  wrote:
> 
> > I was wondering that how I can have for example two different
> > "couple-moltype" in free energy part of my *.mdp file in FEP,
> > alchemical transformation? The reason for having two is to perturb
> > each of them differently in ordered steps.
> 
> You don't quite say what you are trying to do but you can always work
> with more than one topology file.

I got that one wrong.  When you use couple-moltype you obviously want
to make a whole molecule disappear without touching the topology.
Can't you just do two runs with different couple-moltype?

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Re: [gmx-users] couple-moltype in FEP

[Hannes Loeffler]

On Tue, 12 Jul 2016 01:56:42 +0200
Alexander Alexander  wrote:

> I was wondering that how I can have for example two different
> "couple-moltype" in free energy part of my *.mdp file in FEP,
> alchemical transformation? The reason for having two is to perturb
> each of them differently in ordered steps.

You don't quite say what you are trying to do but you can always work
with more than one topology file.
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[gmx-users] couple-moltype in FEP

[Alexander Alexander]

Dear Gromacs user,

I was wondering that how I can have for example two different
"couple-moltype" in free energy part of my *.mdp file in FEP, alchemical
transformation? The reason for having two is to perturb each of them
differently in ordered steps.

Also, would you please confirm me that the "gmx chi ..." can help find out
if the "dihedral angles" of an amino acid changes while adsorbing to a
surface? How much should be the deviation to say it remains unchanged?

Thanks,
Alex
Regards
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