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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
behalf of NG HUI WEN [huiwen...@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-boun...@gromacs.org
[mailto:gmx-users-boun...@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...@nottingham.edu.my
<mailto:huiwen...@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@gromacs.org
<mailto:gmx-users@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-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
<<
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.
>>
<<
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.
>>
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
