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

2020-02-20 Thread 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

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

2020-02-20 Thread 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 -- Gromacs Users mailing list * Please

Re: [gmx-users] couple-moltype

2017-12-08 Thread 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

[gmx-users] couple-moltype

2017-12-08 Thread 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

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

2016-07-12 Thread 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 [

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

2016-07-12 Thread 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

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

2016-07-12 Thread 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 > >

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

2016-07-12 Thread 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

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

2016-07-12 Thread 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

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

2016-07-12 Thread 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

[gmx-users] couple-moltype in FEP

2016-07-11 Thread 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