[gmx-users] questions on distance restraints

[Tsjerk Wassenaar]

Hi Huiwen,

Your approach seems good. Information about the distance restraints will be
printed in the log file from mdrun, or can be extracted from the .edr file.
You can also work your way through the information in the .tpr file given
by gmxdump to see if they are indeed properly defined.

Cheers,

Tsjerk

On Jan 18, 2012 1:46 AM, "NG HUI WEN" <HuiWen.Ng at nottingham.edu.my> wrote:

 Dear gmxusers,****

** **

I have some questions about distance restraints that I hope you would be
able to shed some light on. Thanks in advance.****

** **

I am trying to apply distance restraints to my protein. Below was what I
did:****

** **

-use genrestr to create my ca_disre.itp
genrestr –f membedded_em.gro –o ca_disre.itp –disre (pop-up prompt: CA
atoms selected)****

** **

-in my mdp file****

I added this line near the top: ****

define          = -DDISRES****

** **

-my  top file looks like that****

; Include forcefield parameters****

#include "gromos53a6_lipid.ff/forcefield.itp"****

** **

;Include Protein Topology****

#include "A2a.itp"****

** **

; Include Position restraint file****

#ifdef DISRES****

#include "ca_disre.itp"****

#endif****

;****

#ifdef POSRES****

#include "posre.itp"****

#endif****

;****

** **

;Include POPC topology****

#include "popc.itp"****

#ifdef LIPID_POSRES****

#include "lipid_posre.itp"****

#endif****

** **

;Include water topology****

#include "gromos53a6_lipid.ff/spc.itp"****

** **

#ifdef POSRES_WATER****

; Position restraint for each water oxygen****

[ position_restraints ]****

;  i funct       fcx        fcy        fcz****

   1    1       1000       1000       1000****

#endif****

** **

; Include topology for ions****

#include "gromos53a6_lipid.ff/ions.itp"****

** **

[ system ]****

; Name****

Protein and POPC and Water ****

** **

[ molecules ]****

; Compound        #mols****

Protein_chain_X     1****

POPC              327****

SOL         24767****

CL          11****

** **

The simulation ran without a problem. However, after it was completed, I
compared the final protein structure with the initial and it looked like
the atoms (even the CA atoms , especially those in the loops) had moved
quite a fair bit away from the original position. This made me wonder if
the distance restraints had indeed been applied or perhaps the force
constant was not large enough (default =1000 kJ/mol/nm^2)?  I had checked
the mdout.mdp file “define  = -DDISRES” was there… wasn’t sure how else I
could check this.****

** **

To test whether it was due to the latter, I had tried rerunning the
simulation for 1ns simulation with “disre_fc        = 10000” added to the
mdp file. This time the atoms did not move as far away as previously
observed. ****

** **

I have tried google-ing for the proper way to impose distance restraints
but didn’t find my searches too useful. I wonder if anyone could confirm
with me that the above method is correct/ tell me that I had done something
wrong.****

** **

Cheers for that!****

** **

Best wishes,****

Huiwen****

 ****

** **

** **
 <<

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.
>>

--
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120118/618be24a/attachment.html>