[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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