[gmx-users] Inserting small molecule into the solvated system

[David]

On Fri, 2004-01-02 at 13:18, Semen Esilevsky wrote:
> Dear Gromacs users,
> I've did equilibration of the pure membrane in water
> and now I have to add a small flavone probe to see how
> it incorporates into the membrane. 
> There are two problems:
> 
> 1) How to position the probe. I did it with the
> script, which shifts the coordinates aned then merge 
> pdb files but I suspect that it's possible to do it
> visually. Is it possible with Rasmol or VMD or
> something else?
> 
> 2) I have to delete several water molecules to make a
> hole for the probe. Doing this by hand always lead to
> LINKS warning about more than 30 deg rotation. I tried
> to delete all water and run genbox agin, but with the
> same warning. Then sumulation crashed on step 0.

do you want it on the surface or in the center of the membrane.
Either way growing it using free energy methods is probably the safest
route. This is not well documented though...

> 
> What is a correct way to do the thing?
> 
> --- David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> > On Thu, 1 Jan 2004, Byungchan Kim wrote:
> > 
> > >Hi Folks.
> > >
> > >I want to calculate S2 order parameter with
> > g_rotacf.
> > >>From mailing list discussion, I could figure out
> > how to use g_rotacf on my
> > >purpose. My command is like this,
> > >g_rotacf -f 4pti.trj.xtc -n NH_21.ndx -d -P 2
> > >NH_21.ndx is like this
> > >[NH_21]
> > >329     333
> > >
> > >My problem is that I couldn't get the flat value of
> > correlation function.
> > >The simulation lasted up to 1.5 ns.
> > >What I am curious about is whether the program use
> > orientation of
> > >interatomic vector "in molecular frame". Actually,
> > I am not sure it is a
> > >problem if the program does not use the molecular
> > frame.
> > >I am looking forward to hearing clever answer.
> > 
> > g_rotacf does not use the moleuclar frame. You can
> > try to run the 
> > trajectory through trjconv first, fitting everyhting
> > to reference 
> > structure (and only outputting the protein) and then
> > run g_rotacf.
> > 
> > 
> > >
> > >Thank you very much and Happy New Year.
> > >Byungchan
> > >_______________________________________________
> > >gmx-users mailing list
> > >gmx-users at gromacs.org
> > >http://www.gromacs.org/mailman/listinfo/gmx-users
> > >Please don't post (un)subscribe requests to the
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> > >
> > 
> > -- 
> > David.
> >
> ________________________________________________________________________
> > David van der Spoel, PhD, Assist. Prof., Molecular
> > Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala
> > University.
> > Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> > phone:	46 18 471 4205		fax: 46 18 511 755
> > spoel at xray.bmc.uu.se	spoel at gromacs.org  
> > http://xray.bmc.uu.se/~spoel
> >
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> > 
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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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