Re: [gmx-users] position restraint on a plane

On Wed, 16 Jan 2008 16:12:23 -0500 "Justin A. Lemkul" <[EMAIL PROTECTED]> wrote: Quoting Myunggi Yi <[EMAIL PROTECTED]>: Thank you. I've already read the part, but I was wondering how can I supply my reference z positon in the .itp file. There are no direct way to restrain an atom to stay a

Re: [gmx-users] position restraint on a plane

Quoting Myunggi Yi <[EMAIL PROTECTED]>: > Thank you. > > I've already read the part, but I was wondering how can I supply my > reference z positon in the .itp file. You don't. If you read the link that was provided earlier, or the manual, as has been suggested, you will find that posre.itp does

Re: [gmx-users] position restraint on a plane

Thank you. I've already read the part, but I was wondering how can I supply my reference z positon in the .itp file. I can prepare the "restraint.gro" file manually by placing the atoms at z= 1.0 nm. Then I think I can supply with -r option. Have a great day. On Jan 16, 2008 3:44 PM, Mark Abra

Re: [gmx-users] position restraint on a plane

Myunggi Yi wrote: Where should I put z=1.0 ? Hi Myunggi, The existence of this mailing list doesn't remove the need for you to do your own homework on the wiki, manual or web before firing off a question :-) Table 5.4 defines the format of this line, and section 4.3.1 explains what the k pa

Re: [gmx-users] position restraint on a plane

Myunggi Yi wrote: Thank you. I'm a beginner. How can I setup the restrain? Where should I get the information. The manual is not enough for me. There's even an example of planar restraints in chapter 5. The position restraint .itp file dosen't seem to offer for the reference (z= 1.0) option.

Re: [gmx-users] position restraint on a plane

Where should I put z=1.0 ? On Jan 16, 2008 3:22 PM, Anirban Mudi <[EMAIL PROTECTED]> wrote: > check > http://wiki.gromacs.org/index.php/Position_Restraints > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/lis

[gmx-users] position restraint on a plane

check http://wiki.gromacs.org/index.php/Position_Restraints ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post

Re: [gmx-users] position restraint on a plane

Thank you. I'm a beginner. How can I setup the restrain? Where should I get the information. The manual is not enough for me. The position restraint .itp file dosen't seem to offer for the reference (z= 1.0) option. Whould give me more detail? On Jan 16, 2008 3:14 PM, David van der Spoel <[EMAIL

Re: [gmx-users] position restraint on a plane

Myunggi Yi wrote: Dear users, How can I restrain a certain atoms on a plane? For example, I want to restrain phosphurus atoms of lipid molecules at z=1.0 nm. Is there a way to do this? You can either freeze in one dimension or position restrain to a plane, by setting the force constants appr

[gmx-users] position restraint on a plane

Dear users, How can I restrain a certain atoms on a plane? For example, I want to restrain phosphurus atoms of lipid molecules at z=1.0nm. Is there a way to do this? -- Best wishes, MYUNGGI YI == KLB 419 Institute of Molecular Biophysics Florida State University