ok. Thats the step where I am really confused that how to apply the PR on my system file (system file is a combination of CG protein and CG lipid).
On Tue, Dec 15, 2009 at 12:16 PM, XAvier Periole <[email protected]> wrote: > > Well if you put a protein CG into your DPPC bilayer you'll have to > be soft on the start. PR is one way to do it and you can do similar > to when doing on a atomistic simulation. > > On Dec 15, 2009, at 6:13 PM, sunny mishra wrote: > > Alright thanks. So should I do it for proteins? > > On Tue, Dec 15, 2009 at 12:12 PM, XAvier Periole <[email protected]> wrote: > >> >> No need of position restrained simulation with the CG lipids. >> CG is very forgiving :)) >> >> For proteins it is more delicate. >> >> On Dec 15, 2009, at 6:02 PM, sunny mishra wrote: >> >> Thanks for the reply. I have another quick question that If I have to do >> the Position Restrained EM Simulation of CG DPPC lipid then is it done the >> same way we do for atomistic structure of proteins like by defining the >> LIPPOSRES in the lipid.mdp file or while using MARTINI forcefield is there >> any other way of doing the Position Restrained EM simulation of CG DPPC >> lipids? >> >> On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole <[email protected]>wrote: >> >>> I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's >>>> Website and I am trying to convert the Atomistic structure to CG structure. >>>> For that I am using atom2cg script provided by the martini folks but it >>>> doesn't convert the Atomistic structure to CG structure. atom2cg script >>>> works well for converting the atomistic structure of PROTEIN to CG >>>> structure >>>> of protein but for LIPIDS it doesn't work. Does anyone know how can I >>>> convert the 128 DPPC atomistic structure of lipids to CG structure. >>>> >>>> This is correct. atom2cg is only working for proteins ... >>> >>> I would suggest you take dppc structure file from the martini web site! >>> >>> Best Regards, >>>> >>>> Sunny >>>> >>>> -- >>>> gmx-users mailing list [email protected] >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >>>> >>> >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use thewww >>> interface or send it to [email protected]. >>> >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> >> >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
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