[gmx-users] Re: forward and reverse free energy not consistant (Li Qiang)
Justin A. Lemkul
jalemkul at vt.edu
Mon Jun 16 21:01:31 CEST 2008
The bug report can be found here:
http://bugzilla.gromacs.org/show_bug.cgi?id=175
The thread that gave rise to this report starts here:
http://www.gromacs.org/pipermail/gmx-users/2007-November/030534.html
-Justin
Diana Lousa wrote:
> Hello,
>
> I'm having a similar problem, i.e. inconsistency between forward and
> reverse free energy calculations, in changing the chirality of a
> dihedral. In my case it is unlikely that there is histeresis, given
> that I have a long simulation. Could you be more specific about
> the bug you're referring to, I checked the reported known bugs and
> didn't find anything that was likely to cause this strange results.
>
> Thanks
>
> Diana Lousa
> Instituto de Tecnologia Química e Biológica
> Universidade Nova de Lisboa
> Av. da República – EAN,
> 2780-157 Oeiras
> PORTUGAL
>
>
> ---------- Forwarded message ----------
> From: Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> Date: 2008/6/16
> Subject: Re: [gmx-users] Re: forward and reverse free energy not
> consistant (Li Qiang)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
>
>
> Which GMX version are you using? There's a known bug in version 3.3.1
> that has been fixed in 3.3.3. <http://3.3.3.>
>
> -Justin
>
> friendli wrote:
> >
> > Hi,
> >
> > I use thermodynamics integration. The protocol is 1000step energy
> minimization, 20 ps bond-constraint MD, and then 200ps MD for
> collecting dgdl.
> >
> > thanks
> >
> > Qiang
> >
> > Gerrit Groenhof wrote:
> >>
> >> Looks like hysteresis. Do you do slow growth, or discrete FEP?
> >>
> >> Gerrit
> >>
> >>
> >>
> >>> Dear all Gmxers,
> >>>
> >>> I am calculating a mutation free energy from L<->A for a five AA
> peptides using G96 53a6 force field.
> >>> however, my dG_for and dG_rev is quite different.
> >>> dG_for(lambda=0.00) = - 9.9 kJ/mol
> >>> dG_rev(lambda=1.00) = 1.33 kJ/mol
> >>>
> >>> Is there anything wrong with setting up topologies?
> >>>
> >>> Here is the [atoms] part for morphed atoms. and I attached the
> full .top in the attachment.
> >>> For L->A:
> >>> [ atoms ]
> >>> 17 CH2 2 LEU CB 6 0 14.027
> CH3 0 15.035; qtot 1
> >>> 18 CH1 2 LEU CG 7 0 13.019
> DUM 0 13.019; qtot 1
> >>> 19 CH3 2 LEU CD1 7 0 15.035
> DUM 0 15.035; qtot 1
> >>> 20 CH3 2 LEU CD2 7 0 15.035
> DUM 0 15.035; qtot 1
> >>>
> >>>
> >>> For A->L :
> >>> [ atoms ]
> >>> 17 CH3 2 ALA CB 6 0 15.035
> CH2 0 14.027; qtot 1
> >>> 60 DUM 6 DUM DUM 24 0 13.019
> CH1 0 13.019
> >>> 61 DUM 6 DUM DUM 24 0 15.035
> CH3 0 15.035
> >>> 62 DUM 6 DUM DUM 24 0 15.035
> CH3 0 15.035
> >>>
> >>> thanks for help
> >>>
> >>> LQ
> >>> -------------- next part --------------
> >>> A non-text attachment was scrubbed...
> >>> Name: topol_A2L.top
> >>> Type: application/x-extension-top
> >>> Size: 15230 bytes
> >>> Desc: not available
> >>> Url :
> http://www.gromacs.org/pipermail/gmx-users/attachments/20080616/562fa99f/topol_A2L.bin
> >>> -------------- next part --------------
> >>> A non-text attachment was scrubbed...
> >>> Name: topol_L2A.top
> >>> Type: application/x-extension-top
> >>> Size: 15189 bytes
> >>> Desc: not available
> >>> Url :
> http://www.gromacs.org/pipermail/gmx-users/attachments/20080616/562fa99f/topol_L2A.bin
> >>>
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> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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