Many Thanks Tsjerk, It works
A bientot Stephane ------------------------------ Message: 3 Date: Mon, 25 Feb 2013 13:51:53 +0100 From: Tsjerk Wassenaar <[email protected]> Subject: Re: [gmx-users] Building a box pure solvent with genbox for CG simulations To: Discussion list for GROMACS users <[email protected]> Message-ID: <cabze1sj95gdf-7qjhbekmjsk79rqh2ffp2+s5hbydvxzx4a...@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hi Stephane, martinize.py was written to convert proteins. But you can just take C2+C5+C8 from atomistic decane and energy minimize against the martini topology and you'll be fine. Cheers, Tsjerk On Mon, Feb 25, 2013 at 1:39 PM, ABEL Stephane 175950 <[email protected]> wrote: > Hello All, > > It is a newbie question here, but I can not find a clear response. I would > like to create a simple box of pure DECANE for MD with the Martini force > field. I have tried do that with genbox (as for AA force field) > > genbox_mpi -cp 1_CG_DECANE.pdb -ci 1_CG_DECANE.pdb -o CG_DECANE_box.gro -box > 4.8 4.8 4.8 -nmol 255 -vdwd 0.21 > > where 1_CG_DECANE.pdb file contains three atoms (or beads) for decane. This > atoms C1, C2 and C3 are placed according the geometry given in the > martini_v2.0_solvents.itp file (i.e distance between beads of 4.7 A and angle > of 180o). With this command, only the first atom of the DEC molecule is added > in the box. > > So how to construct of pure solvent when i use the Martini force field > > In addition i have tried to use the martinize python script to transform a > box of decane (AA) -> CG, but seemes to work only for proteins (correct ?). > > Thank you in advance for your help > > Stephane > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
