Re: [gmx-users] Different Lipids into one Moleculetype (for position restrain)

2012-05-19 Thread Ricardo O. S. Soares
Maio de 2012 1:01 Assunto: Re: [gmx-users] Different Lipids into one Moleculetype (for position restrain) Thanks for the corrections. I had to mock up parts of it because usually I only POSRE_RECEPTOR and POSRE_LIGAND. I also have a mix of putting the position restraints in .itp file vs

[gmx-users] Different Lipids into one Moleculetype (for position restrain)

2012-05-18 Thread Ricardo O. S. Soares
Hi everybody, I'm working with a mixed membrane for the first time (POPC+POPE), and I want to restrain the all phosphors  (only Z axis).  However they belong to different [ moleculetype ] (ie. POPC and POPE), and GROMACS does not restrain more than one molecule type at a time. What implications

Re: [gmx-users] Different Lipids into one Moleculetype (for position restrain)

2012-05-18 Thread Jan Marzinek
Why dont you create index files of whatever types you want and then just use in your mdp: freezgrps (from index) and the corresponding directions N N Y Jan On 18 May 2012, at 20:56, Ricardo O. S. Soares ross_...@yahoo.com.br wrote: Hi everybody, I'm working with a mixed membrane for the

Re: [gmx-users] Different Lipids into one Moleculetype (for position restrain)

2012-05-18 Thread Justin A. Lemkul
On 5/18/12 3:56 PM, Ricardo O. S. Soares wrote: Hi everybody, I'm working with a mixed membrane for the first time (POPC+POPE), and I want to restrain the all phosphors (only Z axis). However they belong to different [ moleculetype ] (ie. POPC and POPE), and GROMACS does not restrain more

Re: [gmx-users] Different Lipids into one Moleculetype (for position restrain)

2012-05-18 Thread Justin A. Lemkul
On 5/18/12 10:28 PM, Peter C. Lai wrote: Synopsis: position restraints are coupled to the moleculetype. So you need to define position restraints individually for each molecule type contiguous with their topologies. There's a couple of ways to do it, using some simple #include and #define:

Re: [gmx-users] Different Lipids into one Moleculetype (for position restrain)

2012-05-18 Thread Peter C. Lai
Thanks for the corrections. I had to mock up parts of it because usually I only POSRE_RECEPTOR and POSRE_LIGAND. I also have a mix of putting the position restraints in .itp file vs. in the topol.top, depending on how often I am changing my topol.top (things like genion and g_membed modify them).