[gmx-users] The solvation free energy of a vdw ligand

[Tanping Li]

Hey Justin,

Thanks for the help. I've generated big size of data so I hope I can find the way to fix the problem before transfer to the new version.

I just find that it gives me problem when I use the self-defined atom type in the state B, however works fine if I use the existing atom type in the state B.

I defined the atom types by the following way:

[ atometypes ]
;name      mass     charge  Ptype  C6  C12
dum_CH3    15.035     0       A     0   0
....
....


Did I missed some there? I noticed that the "at. num" is included in the ffgmxnb.itp file. I searched the manual, but haven't find that.


Tanping  



--- On Fri, 2/17/12, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] The solvation free energy of a vdw ligand
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Friday, February 17, 2012, 10:14 AM
> 
> 
> Tanping Li wrote:
> > Dear all,
> > 
> > I posted the message yesterday and haven't get a
> response. My trouble is that: when I calculate the solvation
> free energy of a vdw ligand, the energy of lambda=0 varies
> with different state B. Does anyone has the similar
> experience? I greatly appreciate your help since I tried a
> lot but haven't find the reason.
> > 
> > 
> 
> Version 3.3.1 is ancient, and there may well be a bug that
> has since been fixed in the intervening years.  Try
> again with version 4.5.5 (though there are significant
> changes in the way the free energy code works, it should not
> affect the simple test you've proposed).
> 
> -Justin
> 
> > Yours
> > Tanping     
> > 
> > 
> > --- On Thu, 2/16/12, Tanping Li <jia_11_osu at yahoo.com>
> wrote:
> > 
> >> From: Tanping Li <jia_11_osu at yahoo.com>
> >> Subject: [gmx-users] The free energy of vdw part
> >> To: gmx-users at gromacs.org
> >> Date: Thursday, February 16, 2012, 11:28 AM
> >> Dear gmx users,
> >> 
> >> I am calculating the free energy of solvating a
> small ligand
> >> by water, using FEP method. The free energy is
> separated
> >> into the contribution of electric+vdw. I find
> problem for
> >> the vdw part.
> >> 
> >> I am using gromacs-3.3.1. In the top file, I set
> the state B
> >> of ligand where LJ parameters of atoms are zero; in
> the mdp
> >> file, I set the lamda=0.
> >> 
> >> According to my understanding, above setting should
> gives me
> >> the energy of ligand's state A. However, when I
> calculate
> >> the energy with a mdp with "free_energy=No" and a
> top
> >> without setting the B state, I get a very different
> energy.
> >> 
> >> I tried but haven't dig out which part I missed. I
> greatly
> >> appreciate your help and consideration on this
> issue.
> >> 
> >> 
> >>  
> >>    -- gmx-users mailing list   
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> 
> -- ========================================
> 
> 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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