[gmx-users] energy of conformation change in water box

Tue Oct 18 04:51:23 CEST 2005

Hi guys,

I wonder if someone could help me with an issue I've been mulling.  I want
to determine how much energy is required to move a protein from a given
conformation A to a slightly different conformation B.  Currently I am
taking structure A, equilibrating, then simply changing the coordinates to
make structure B.  I then make a new water box for structure B and
equilibrate (doing all the standard steps, including em and pr runs).  

Currently I am simply taking the intramolecular energy terms.  Really, I
think I should take the total energy, including solvent.  However if the
number of solvent molecules changes from A to B, then this number will not
make sense.  On the other hand, if one were to force the number to remain
constant, what thermodynamic variable should be freed? Pressure? Volume?  If
pressure is held constant, then volume must change, and then there is the
matter of calculating work done on the environment.  Really I would prefer a
simple solution right now, since I'm at an early stage of my project.

If anyone has some advice it will be appreciated.

Thanks  

Sam  

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of lmao
Sent: Monday, October 17, 2005 10:15 PM
To: gmx-users at gromacs.org
Cc: gmx-users at gromacs.org
Subject: Re: [gmx-users] Fatal error: Atomtype 'K' not found!

Because I will include decane as solvent and I don't have topology file for
decane. Or I should build one. Thanks for your comment.

mao  
> 
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> Hi,
> 
> 
> > I was using Gromacs-3.2-1 for peptide simulations. I first used  
> > "pdb2gmx" to generate .gro file and I chose 5 from the following  
> > options to include H
> > "Select the Force Field:
> >  0: GROMOS96 43a1 Forcefield (official distribution)
> >  1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
> >  2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
> >  3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> >  4: Gromacs Forcefield (see manual)
> >  5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new  
> > runs)"
> 
> Question: I assume you read the entire last line here. Why do you  
> need to use ffgmx2 and not e.g. OPLS?
> 
> Cheers,
> 
> Erik
> 
> -----------------------------------------------------------
> Erik Lindahl  <lindahl at sbc.su.se>
> Assistant Professor, Stockholm Bioinformatics Center
> Stockholm University, SE 106 91 Stockholm
> Phone: +46 8 5537 8564     Fax: +46 8 5537 8214
> 
> 
> 
> 
> 
> --Apple-Mail-1-962561109
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> <HTML><BODY style=3D"word-wrap: break-word; -khtml-nbsp-mode: space; =
> -khtml-line-break: after-white-space; "><DIV><BLOCKQUOTE =
> type=3D"cite"></BLOCKQUOTE><DIV><FONT class=3D"Apple-style-span" =
> color=3D"#0000DD">Hi,</FONT></DIV><BR><BR><BLOCKQUOTE type=3D"cite"><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; min-height: 14px; "></DIV><DIV style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I was =
> using Gromacs-3.2-1 for peptide simulations. I first used "pdb2gmx" to =
> generate .gro file and I chose 5 from the following options to include =
> H</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: =
> 0px; margin-left: 0px; ">"Select the Force Field:</DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; "><SPAN class=3D"Apple-converted-space">=A0</SPAN>0: =
> GROMOS96 43a1 Forcefield (official distribution)</DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; "><SPAN class=3D"Apple-converted-space">=A0</SPAN>1: =
> GROMOS96 43b1 Vacuum Forcefield (official distribution)</DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; "><SPAN class=3D"Apple-converted-space">=A0</SPAN>2: =
> GROMOS96 43a2 Forcefield (development) (improved alkane =
> dihedrals)</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
> margin-bottom: 0px; margin-left: 0px; "><SPAN =
> class=3D"Apple-converted-space">=A0</SPAN>3: OPLS-AA/L all-atom force =
> field (2001 aminoacid dihedrals)</DIV><DIV style=3D"margin-top: 0px; =
> margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN =
> class=3D"Apple-converted-space">=A0</SPAN>4: Gromacs Forcefield (see =
> manual)</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
> margin-bottom: 0px; margin-left: 0px; "><SPAN =
> class=3D"Apple-converted-space">=A0</SPAN>5: gmx Forcefield with =
> hydrogens for NMR stuff (Do NOT use for new =
> runs)"</DIV></BLOCKQUOTE></DIV><DIV><FONT class=3D"Apple-style-span" =
> color=3D"#0000DD"><BR =
> class=3D"khtml-block-placeholder"></FONT></DIV>Question: I assume you =
> read the entire last line here. Why do you need to use ffgmx2 and not =
> e.g. OPLS?<DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV>Erik<DIV><DIV><BR><DIV> =
> <SPAN class=3D"Apple-style-span" style=3D"border-collapse: separate; =
> border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; =
> font-size: 12px; font-style: normal; font-variant: normal; font-weight: =
> normal; letter-spacing: normal; line-height: normal; text-align: auto; =
> -khtml-text-decorations-in-effect: none; text-indent: 0px; =
> -apple-text-size-adjust: auto; text-transform: none; orphans: 2; =
> white-space: normal; widows: 2; word-spacing: 0px; =
>
"><DIV>-----------------------------------------------------------</DIV><D=
> IV>Erik Lindahl=A0 &lt;<A =
>
href=3D"mailto:lindahl at sbc.su.se">lindahl at sbc.su.se</A>&gt;</DIV><DIV>Assi=
> stant Professor, Stockholm Bioinformatics Center</DIV><DIV>Stockholm =
> University, SE 106 91 Stockholm</DIV><DIV>Phone: +46 8 5537 8564=A0 =A0 =
> =A0Fax: +46 8 5537 8214</DIV><DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><BR =
> class=3D"Apple-interchange-newline"></SPAN> =
> </DIV><BR></DIV></DIV></DIV></BODY></HTML>=
> 
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