I just applied genrestr command: #genrestr -f minim.gro -o water_posre.itp -fc 100000 100000 100000 And then I just chose the water to create the water_posre.itp. Would not that work?
Sincerely, Shima ________________________________ From: Mark Abraham <[email protected]> To: Shima Arasteh <[email protected]>; Discussion list for GROMACS users <[email protected]> Sent: Sunday, June 2, 2013 3:35 PM Subject: Re: [gmx-users] water position restraints What's in that .itp? You can only restrain all the waters that have that moleculetype. See http://www.gromacs.org/Documentation/How-tos/Position_Restraints On Sun, Jun 2, 2013 at 9:52 AM, Shima Arasteh <[email protected]> wrote: Dear GMX users, > >I' d like to put the position restraints on water oxygen atoms. >To do so, I made a water_posre.itp file. Then I modified the top file, as >this, but didn't work: > > >#ifdef POSRES_WATER >; Position restraint for each water oxygen >[ position_restraints ] >; i funct fcx fcy fcz > 1 1 1000 1000 1000 >#include "water_posre.itp" >#endif > > >Would you please help me here? I don't know how I change the fcx, fcy, and >fcz. Is it possible to change the fc values 1000 to 100000 in top file by just >text editing as below: > >#ifdef POSRES_WATER >; Position restraint for each water oxygen >[ position_restraints ] >; i funct fcx fcy fcz > 1 1 100000 100000 100000 >#include "water_posre.itp" >#endif > > > > > > >Sincerely, >Shima >-- >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 > -- 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
