[gmx-users] Problem with position restraints£¡£¡£¡£¡£¡£¡

[David]

On Sun, 2003-10-19 at 14:48, nanyu101 wrote:
> Dear gmx-users,
>     I am doing simulation for an ion channel in lipid bilayer. Now, I want to restraint the ion channel(not a normal ion channel) for the water molecules entering the channel. I just did as follows:
> 1.create a  posre.itp file for my ion channel and rename it as posre_phb.itp.
> 
> 2.edit the ion.top file.
> 
> ;include forcefield parameters
> #include "ffG43a2.itp"
> #include "dpp.itp"
>  
> #ifdef POSRES
> #include "posre.itp"
> #endif
>  
> #include "phb.itp"
> #ifdef POSRE_PHB
> #include "posre_phb.itp"
> #endif
>  
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
> 
> 3.edit the md.mdp file as define = -DPOSRE_PHB.
> 4. run grompp to create the tpr file.
> 5. run gmxdump to check the tpr file.And then,I found that the force matrix in gmxdump outfile is all zero.
> 
> 
>       f[ 5636]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>       f[ 5637]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
> So,I think my position restrain failed. After I run the dynamics, my ion channel topology was distorted just as my expectation.
> 
the force in the tpr file is always zero,since it is an input file.
Check whether your tpr contains POSRES at the right atom numbers
Also check the force constant, 100-1000 kJ/mole should be enough.


> Would you please give some comments? THanks a lot.
> 
> 
> 
> ______________________________________
> Best wishes,
> nanyu
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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