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
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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Gromacs Users mailing list
* Please
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
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
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 [
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
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
> >
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
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
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
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
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