[gmx-users] Multiple position restraints on the same system

[NG HUI WEN]

Dear GMXusers,

 

I am trying to perform NVT on my solvated protein-lipid system. After
inserting the protein into the lipid using inflategro and a round of
energy minimization, I performed a 100ps NVT with position restraint
only on the protein molecule using (posre.itp).

 

After 100ps of NVT, the bilayer separated. As a result, I am now trying
to redo the NVT step, this time probably with position restraints on the
protein AND the P8 atom of my POPC (lipid_posre.itp). 

 

I have in my .top file

;Protein

#include "protein.itp"

#ifdef POSRES

#include "posre.itp"

#endif

 

;Lipid

#include"popc.itp"

#ifdef POSRES_LIPID

#include "lipid_posre.itp"

#endif

 

When it comes to the .mdp file, I wonder how do I include both 

define = -DPOSRES and define = -DPOSRES_LIPID ? 

 

Another quick question, is it advisable to do "trjconv -pbc mol" on my
system after every energy minimization/ MD to get an unbroken structure
before I carry on further?

 

Thanks a lot

 

HW

 

<< This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. 

This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK & Malaysia legislation. >>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101027/11798c78/attachment.html>