[gmx-users] Position restraint file

Kai Zhuang kai.zhuang at gmail.com
Fri Aug 12 17:26:02 CEST 2005


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
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> 
>  
>  
>  Regards, 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> 
> 
>  
>  
>  
>  
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> 
> 


-- 
Confidentiality Notice:
If you are not the intended receipient of this email, please do not
disclose its information
and notify the sender immediantely.  Failure to comply may result in
legal actions.

Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
6478314789



More information about the gromacs.org_gmx-users mailing list