[gmx-users] TFE-water simulation

[Archana Sonawani-Jagtap]

Thanks Joao Henriques for helping me with the steps.
On Nov 4, 2013 3:18 PM, "João Henriques" <joao.henriques.32353 at gmail.com>
wrote:

> Hello Archana,
>
> I'm also toying with a TFE-water system, therefore I am also a newbie. This
> is what I am doing, I hope it helps:
>
> 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I
> don't use PRODGR, see why in DOI: 10.1021/ci100335w).
> 2) Do the math and check how many molecules of TFE you're going to need for
> a given v/v TFE-water ratio and a given simulation box volume.
> 3) Build box with the correct size.
> 4) Randomly insert correct number of TFE molecules.
> 5) Solvate.
> 6) Insert protein.
>
> Hopefully, the amount of TFE and water molecules that will be deleted in
> inserting the protein in the final step will be proportional, given that
> the TFE molecules are well distributed.
>
> I've tried many different ways of doing this and it's always impossible to
> maintain a perfect TFE-water ratio, no matter the order and manner of
> insertion of each system component. I've also never been able to insert the
> correct number of waters after the TFE. My calculations predict a higher
> number, but the solvation algorithm can't find enough space for them.
>
> In sum, either you place each molecule by hand and you spend a life time
> building the system, or you just make a few compromises and deal with it. I
> ended up going with the former as I have a limited amount of time on my
> hands and I am aware of the approximations I am doing.
>
> Best regards,
>
> João Henriques
> ------------------------------------------------
> PhD student
> Division of Theoretical Chemistry
> Lund University
> Lund, Sweden
> ------------------------------------------------
> joao.henriques at teokem.lu.se
> http://www.teokem.lu.se/~joaoh/
>
>
> On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote:
> >
> >> Dear Justin,
> >>
> >> I have not constructed the system but I have downloaded it from ATB
> >> website. To maintain the number of TFE and water molecules(1:1 v/v) in
> the
> >> system (I don't want to add extra water molecules) I tried many options
> in
> >> genbox but still it adds 678 water molecules. Can you provide me some
> >> hint?
> >>
> >>
> > Not without seeing your actual command(s).
> >
> >
> >  Is their need to remove periodicity of this pre-equilibrated system as
> in
> >> case of lipids?
> >>
> >>
> > No idea.  Are the molecules broken in the initial configuration?
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> >
> > Justin A. Lemkul, Ph.D.
> > Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >
> > ==================================================
> >
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