[gmx-users] problem about position restrain

[Daniel Larsson]

On Feb 21, 2008, at 13:27, Justin A. Lemkul wrote:

> Quoting sudheer babu <sudheer.pbm07 at gmail.com>:
>
>> Hi gmx users,
>> I am trying to run position restrain step for protein embedded in  
>> popc. is
>> it possible to do position restrain at a time for both popc and  
>> protein like
>> below mentioned here?
>> in " .top " file
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "lip_posre.itp"
>> #include "posre.itp"
>> #endif
>
> I don't know, have you tried it?  Does it seem to work?  Something  
> that I have
> done before is the following:
>
> ; position restrain protein
> #ifdef POSRES
> #include posre.itp
> #endif
>
> ; position restrain lipid
> #ifdef POSRES_LIPID
> #include lipid_posre.itp
> #endif
>

Just remember to put each position restrain entry under the correct  
molecule definition (called [ moleculetype ]) in the relevant .top  
or .itp files. You can find out about the details in chapter 5.6 of  
the Gromacs manual.

> That way, you can define both, or only one throughout the course of  
> minimization
> and equilibration, i.e.:
>
> define   = -DPOSRES -DPOSRES_LIPID
>
> or
>
> define   = -DPOSRES
>
> -Justin
>
>>
>> or any other way to do position restrain for both.
>> pls help me.....
>> Thanks in advance
>>
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
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---

Daniel Larsson
Molecular Biophysics group
Department of Cell and Molecular Biology
Uppsala University

+46-18-471 4006 (phone)
+46-18-511 755  (fax)
http://xray.bmc.uu.se/~larsson
larsson at xray.bmc.uu.se