[gmx-users] questions on distance restraints

NG HUI WEN HuiWen.Ng at nottingham.edu.my
Mon Jan 30 15:26:05 CET 2012


Hi Justin,

Thanks - the simulation is running now after I added the -pd flag. Cheers for your help!

Huiwen

________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: 30 January 2012 22:14
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] questions on distance restraints

NG HUI WEN wrote:
> 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?
>
>

Some nodes are dedicated to doing PME calculations.  The problem is distance
restraints can't be split across DD cells; the restraint thus sets the minimum
size of a DD cell.  You can either manipulate the DD cell properties (using the
options shown in the error message) or you can make life much easier and use
particle decomposition (mdrun -pd).  It will run slightly slower than DD, but
there's no need to tweak a whole bunch of parameters (which will ultimately end
up in performance loss anyway).

-Justin

>
> 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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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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