Erratum: Where I wrote "I ended up going with the former" it should be "I ended up going with the latter".
/J On Mon, Nov 4, 2013 at 10:47 AM, João Henriques < joao.henriques.32...@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.henriq...@teokem.lu.se > http://www.teokem.lu.se/~joaoh/ > > > On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul <jalem...@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 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> >> ================================================== >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists