[gmx-users] questions on distance restraints

Mon Jan 30 14:56:01 CET 2012

Dear all,

Apologies for getting back to this topic again - am still having trouble trying to get distance restraints to work on my protein.

Following Tsjerk's advice, I have

1)put the tpr file through gmxdump:

   disre                = No
   disre_weighting      = Conservative
   disre_mixed          = FALSE
   dr_fc                = 10000

2)there was no distance restraint information on the edr file (no surprise considering the above)

I have then tried inserting "disre = simple" in my mdp file and attempted to run the simulation.

mpisub 1 test.jif

(note that 1 = 8 cpus)

Unfortunately, I got the following error:

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 11.8602 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I also tried changing the number of cpus

mpisub 2 test.jif

(2=16 cpus)

The error was

Fatal error:
There is no domain decomposition for 10 nodes that is compatible with the given box and a minimum cell size of 11.8602 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I dont understand why the error stated 10 instead of 16 nodes. Removing "disre=simple" will allow the simulation to run smoothly. Can anyone enlighten me on how to apply distance restraints properly?

Many thanks.

Huiwen

________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of NG HUI WEN [HuiWen.Ng at nottingham.edu.my]
Sent: 18 January 2012 16:40
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] questions on distance restraints

Dear Tsjerk,

Thanks very much indeed for confirming this, really appreciate it. I will do as you suggest to have a more thorough check.

Best wishes,
Huiwen

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Tsjerk Wassenaar
Sent: Wednesday, January 18, 2012 1:08 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] questions on distance restraints

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<mailto: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

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