[gmx-users] Position restraint file

[Kai Zhuang]

hmmm, that makes sense. thx.

On 8/12/05, Yang Ye <leafyoung81-group at yahoo.com> wrote:
>  Kai Zhuang wrote: 
>  #include "A.top" //itp shall be the correct suffix
> #ifdef POSRES_A //define them separatedly
> #include "A_posre.itp"
> #endif
> 
> #include "B.top"
> #ifdef POSRES_B
> #include "B_posre.itp"
> #endif
> 
> ya you're right, 
> should define them seperately since you're going to be putting
> restrain on only one of them.
> would suffix "top" not work? i actually did use itp in my system, but
> i didn't think there's any real difference between itp and top suffix
> and they're treated the same.
>  
>  The reason why separating them is *not* because "putting restrain on only
> one of them". But because [ position_restrains ] section is part of
> molecular defition, which should be followed after the [ moleculetype ], [
> atoms ] and other sections. The C preposessor used by grompp has done the
> magic to provide the flexibility of using #include. If cpp is not around,
> you should have everything for one molecule together.
>  
>  The suffix does not matter the processing. But for molecular defintion, itp
> is the right name to go with.
> 
>  
>  
>  On 8/12/05, Yang Ye <leafyoung81-group at yahoo.com> wrote:
>  
>  
>  Kai Zhuang wrote: 
>  i did this when i was working on a similar system:
> 
> create 2 pdb filies (1 DNA, 1 nanotube), call it A.pdb, B.pdb
> do pdb2gmx twice, get 2 gro files, 2 top files, 2 posre.itp files.
> cat the 2 gro files together, edit the file, fix the atom number
> manually. call it C.gro
> create a new top file that connects the four topology files together,
> call it C.top
> 
> #include "A.top"
> #include "B.top"
> 
> #ifdef POSRES
> #include "A_posre.itp"
> #include "B_posre.itp"
> #endif
>  
>  I don't feel this alright. position_restrains section shall be part of the
> molecular defintion.
>  
>  #include "A.top" //itp shall be the correct suffix
> #ifdef POSRES_A //define them separatedly
> #include "A_posre.itp"
> #endif
> 
> #include "B.top"
> #ifdef POSRES_B
> #include "B_posre.itp"
> #endif
> 
>  in md.mdp, you can make a selection for -DPOSRES_A, or -DPOSRES_B, or both.
>  
>  look at A.top and B.top, any overlapping declarations, put them in C.top.
> basically, you want to strip A.top and B.top to just the information
> about the atoms.
> leave the A_posre.top and B_posre.top be.
> 
> should work.
> 
> On 8/11/05, Bob Johnson <robertjo at physics.upenn.edu> wrote:
>  
>  
>  Hello,
> I am studying the interactions between single stranded DNA and a carbon
> nanotube. I am using the Amber force field for the DNA molecule. When the
> two
> systems (dna and nanotube) are brought together, the nanotube is severely
> deformed by the presence of the dna. I wanted to try restraining the
> positions
> of the nanotube since it is probable that the nanotube structure remains the
> same upon insertion of a dna molecule. How would I format the posre.itp
> file?
> Do I specify the coordinates of all the nanotube carbon atoms along with a
> force constant? I'm unsure of the syntax.
> Thanks,
> Bob Johnson
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>  
>  Regards, 
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Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
6478314789