Re: [gmx-users] Domain Decomposition Error

Could be a bug, but unless you can reproduce it with 4.5.7 or 4.6.x then you won't get much help there :-) Mark On Fri, May 31, 2013 at 9:56 PM, Parker de Waal wrote: > Hi Everyone, > > I'm trying to run energy minimization on my system and I am encountering > the following error: > > Getting L

Re: [gmx-users] domain decomposition trick for highly parallel non-equilibrium runs

On Sat, Oct 6, 2012 at 6:03 PM, Dr. Vitaly Chaban wrote: > Would anyone perhaps suggest some tricks to increase the stability of > the highly parallel jobs (NP > 100), which use domain decomposition > among nodes. It would be more helpful to know what you are talking about, i.e. a definition of s

Re: [gmx-users] Domain decomposition error, is mdrun_mpi now obsolete?

There are 2 ways to build a parallel gromacs. For shared memory clusters you still need to use MPI, but if all your cores are on one host, you can build it without MPI which will make an mdrun that uses threading. Domain Decomposition is tied in with the size of the simulation and PME, so it's no

Re: [gmx-users] Domain decomposition error, is mdrun_mpi now obsolete?

On 9/22/12 6:05 PM, Ladasky wrote: Hello again everyone, I'm currently running GROMACS 4.5.4 on Ubuntu Linux 11.10. I'm trying to clean up my simulation conditions. Many of my MDP files are hold-overs from earlier versions of GROMACS, as far back as v. 3.3. I have written some shell scripts

Re: [gmx-users] Domain decomposition problems

On 25/02/2012 4:52 AM, Olivia Waring wrote: Dear Gromacs users, Could someone please shed light on the following problem? My system consists of an alkanethiol SAM (in the xy plane) with a layer of water on top. The mdrun command works when the box vectors are 1.1, 1.3, and 2.5, but the SAM fl

Re: [gmx-users] Domain decomposition in FEP

On 15/02/2012 1:44 AM, lloyd riggs wrote: Dear Alexey Zeifman, > From my experience it is just the nodes have to break down into some sort of even multiple by dividing the domain decomposition size or vise versi. I think somone elses answere was just to try it with a couple sizes for the deco

Re: [gmx-users] Domain decomposition in FEP

Alexey Zeifman wrote: Dear all, I'm trying to run FEP calculation of the ligand in the protein in water. Performing NVT-dynamics for Lennard-Johnes perturbation using soft core results in the following error: There is no domain decomposition for 20 nodes... I've checked out the log-file a

Re: [gmx-users] Domain decomposition in FEP

Dear Alexey Zeifman, >From my experience it is just the nodes have to break down into some sort of >even multiple by dividing the domain decomposition size or vise versi. I >think somone elses answere was just to try it with a couple sizes for the >decomposition, as multiples of the number of

Re: [gmx-users] Domain decomposition error in alchemical free energy perturbation MD

On Sat, Oct 15, 2011 at 2:11 PM, Xiaoxiao He wrote: > Dear all, > I'm doing an "slow-growth" alchemical free energy perturbation calculation > of the formation of a disulfide bridge between two Cysteines with Gromacs. > I've had tried different ways to combine the topology of both state A and > st

Re: [gmx-users] domain decomposition

On 5/04/2011 5:39 PM, mohsen ramezanpour wrote: Dear Mark Thank you for your important notes,I didn't know them. Then,Can it be resulted from your sentences , there is not any way for doing simulation with only some parts of a protein? What can I do if I need simulating only ACTIVE SITE of a

Re: [gmx-users] domain decomposition

Dear Mark Thank you for your important notes,I didn't know them. Then,Can it be resulted from your sentences , there is not any way for doing simulation with only some parts of a protein? What can I do if I need simulating only ACTIVE SITE of a protein?Do I have to simulate the whole of protein

Re: [gmx-users] domain decomposition

On 5/04/2011 5:09 PM, mohsen ramezanpour wrote: Dear Mark Actually I don't know why. I just did the normal process as other my simulations. Let me discribe my work in details: I had a protein and a drug,I separated all residues around my drug (2 nm in radius) by PYMOL You can't do that and h

Re: [gmx-users] domain decomposition

Dear Mark Actually I don't know why. I just did the normal process as other my simulations. Let me discribe my work in details: I had a protein and a drug,I separated all residues around my drug (2 nm in radius) by PYMOL Then I saved the result as protein-new.pdb So.I used pdb2gmx to generate .to

Re: [gmx-users] domain decomposition

On 4/04/2011 1:51 AM, mohsen ramezanpour wrote: Dear All I have a file which contains afew residues (noncontinuous), When I use mdrun on a computer(4 cpu) I am facing with the following Error: Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and

Re: [gmx-users] domain decomposition error

Moeed wrote: Hello Justin, I am running in parallel but this error comes up with 8, 7, 6, 5, 4 and even 3 number of processors. I read about domain decomposition on the website and tried less number of processors, as just mentioned. My understanting after reading about the error is that par

Re: [gmx-users] Domain decomposition configuration

Mark Abraham wrote: On 10/02/2011 12:45 PM, Justin A. Lemkul wrote: Mark Abraham wrote: On 10/02/2011 8:10 AM, Justin A. Lemkul wrote: Denny Frost wrote: Is tpbconv with the "pbc" option the best way to make the molecules whole again? The only way, as far as I'm aware (aside from ed

Re: [gmx-users] Domain decomposition configuration

On 10/02/2011 12:45 PM, Justin A. Lemkul wrote: Mark Abraham wrote: On 10/02/2011 8:10 AM, Justin A. Lemkul wrote: Denny Frost wrote: Is tpbconv with the "pbc" option the best way to make the molecules whole again? The only way, as far as I'm aware (aside from editconf's crude approac

Re: [gmx-users] Domain decomposition configuration

Mark Abraham wrote: On 10/02/2011 8:10 AM, Justin A. Lemkul wrote: Denny Frost wrote: Is tpbconv with the "pbc" option the best way to make the molecules whole again? The only way, as far as I'm aware (aside from editconf's crude approach). Do this before you concatenate your systems.

Re: [gmx-users] Domain decomposition configuration

On 10/02/2011 8:10 AM, Justin A. Lemkul wrote: Denny Frost wrote: Is tpbconv with the "pbc" option the best way to make the molecules whole again? The only way, as far as I'm aware (aside from editconf's crude approach). Do this before you concatenate your systems. And you will then ha

Re: [gmx-users] Domain decomposition configuration

Denny Frost wrote: Is tpbconv with the "pbc" option the best way to make the molecules whole again? The only way, as far as I'm aware (aside from editconf's crude approach). Do this before you concatenate your systems. -Justin On Wed, Feb 9, 2011 at 2:06 PM, Justin A. Lemkul

Re: [gmx-users] Domain decomposition configuration

Is tpbconv with the "pbc" option the best way to make the molecules whole again? On Wed, Feb 9, 2011 at 2:06 PM, Justin A. Lemkul wrote: > > > Denny Frost wrote: > >> This run is actually a combination of two 5x5x5 nm boxes, one if which was >> previously run in DD, and the other is water. Sinc

Re: [gmx-users] Domain decomposition configuration

Denny Frost wrote: This run is actually a combination of two 5x5x5 nm boxes, one if which was previously run in DD, and the other is water. Since the length of that bond is almost 5 nm, is it possible that the pbc's are not being recognized? There is no way I have a bond that long from my p

Re: [gmx-users] Domain decomposition configuration

This run is actually a combination of two 5x5x5 nm boxes, one if which was previously run in DD, and the other is water. Since the length of that bond is almost 5 nm, is it possible that the pbc's are not being recognized? There is no way I have a bond that long from my previous run. On Wed, Feb

Re: [gmx-users] Domain decomposition configuration

Denny Frost wrote: I'm using version 4.5.3 Here's the output from the log file from DD initiation to the error: Initializing Domain Decomposition on 8 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances:

Re: [gmx-users] Domain decomposition configuration

I'm using version 4.5.3 Here's the output from the log file from DD initiation to the error: Initializing Domain Decomposition on 8 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded in

Re: [gmx-users] Domain decomposition configuration

Denny Frost wrote: I am trying to start a run using domain decomposition on a 5x5x10 nm box with about 26,000 atoms in it. I've tried running 8-16 pp nodes, but gromacs always throws an error saying that there is no domain decomposition compatible with this box and a minimum cell size of 6.7

Re: [gmx-users] domain decomposition error

On 18/11/2010 12:07 AM, Fabio Affinito wrote: Hi, I'm trying to run a simulation with 4.5.3 (double precision) on bluegene. Double precision comes with a big performance penalty, particularly on BlueGene. Don't use it unless you know you need it. I get this error: NOTE: Turning on dynami

Re: [gmx-users] Domain decomposition error

: nishap.pa...@utoronto.ca Date: Monday, May 17, 2010 10:28 Subject: Re: [gmx-users] Domain decomposition error To: gmx-users@gromacs.org Thanks Justin. But how come it worked for methanol. The system is of the same size , and all the parameters are same, so I don't understand why it won&#

Re: [gmx-users] Domain decomposition error

- Original Message - From: nishap.pa...@utoronto.ca Date: Monday, May 17, 2010 10:28 Subject: Re: [gmx-users] Domain decomposition error To: gmx-users@gromacs.org > Thanks Justin. But how come it worked for methanol. The system > is of the same size , and all the parameters are sa

Re: [gmx-users] Domain decomposition error

nishap.pa...@utoronto.ca wrote: Thanks Justin. But how come it worked for methanol. The system is of the same size , and all the parameters are same, so I don't understand why it won't work for ethanol. I don't know. The DD algorithm is rather complex, and beyond the information in the man

Re: [gmx-users] Domain decomposition error

Thanks Justin. But how come it worked for methanol. The system is of the same size , and all the parameters are same, so I don't understand why it won't work for ethanol. Quoting "Justin A. Lemkul" : nishap.pa...@utoronto.ca wrote: Hello, I got this following error when I was trying t

Re: [gmx-users] Domain decomposition error

nishap.pa...@utoronto.ca wrote: Hello, I got this following error when I was trying to run a simulation of ethanol-water box size 4*4*4 nm (~6530 atoms). Fatal error: There is no domain decomposition for 14 nodes that is compatible with the given box and a minimum cell size of 0.62175 n

Re: [gmx-users] domain decomposition

Hi Try with -dd 2 x 2 x 2 option with 8 nodes and check the performance. I too got the same problems, i could overcome with symmetrical -dd option. Srinivas. On Fri, May 7, 2010 at 8:57 AM, irene farabella < i.farabe...@mail.cryst.bbk.ac.uk> wrote: > Hello! > > I am new to Gromacs and especiall

Re: [gmx-users] domain decomposition and load balancing

es the log file say? > > Mark > > > On Fri, Feb 19, 2010 at 3:16 PM, Mark Abraham > wrote: > > > - Original Message - > > > From: "Justin A. Lemkul" > > > Date: Saturday, February 20, 2010 10:13 > > > Subject: Re: [gmx-users] d

Re: [gmx-users] domain decomposition and load balancing

- Original Message - From: Amit Choubey Date: Saturday, February 20, 2010 10:25 Subject: Re: [gmx-users] domain decomposition and load balancing To: Discussion list for GROMACS users > Hi Mark and Justin, > I am using a box of size (20nm)x(20nm)x(60nm)..system is open alon

Re: [gmx-users] domain decomposition and load balancing

number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition Amit On Fri, Feb 19, 2010 at 3:16 PM, Mark Abraham wrote: > - Original Message - > From: "Justin A. Lemkul" > Date: Saturday, February 20, 2010 10:13 > Subject:

Re: [gmx-users] domain decomposition and load balancing

- Original Message - From: "Justin A. Lemkul" Date: Saturday, February 20, 2010 10:13 Subject: Re: [gmx-users] domain decomposition and load balancing To: Discussion list for GROMACS users > > > Amit Choubey wrote: > >Hi Mark, > > > >I am not using

Re: [gmx-users] domain decomposition and load balancing

Amit Choubey wrote: Hi Mark, I am not using PME calculation. I was hoping mdrun will do the cell allocation itself. It will, unless it can't, which is exactly your problem. Mark's point stands, regardless of whether or not you're using PME. DD requires certain minimum size requirements

Re: [gmx-users] domain decomposition and load balancing

Hi Mark, I dont think i need to play with npme at all. Amit On Fri, Feb 19, 2010 at 2:41 PM, Amit Choubey wrote: > Hi Mark, > > I am not using PME calculation. > > I was hoping mdrun will do the cell allocation itself. > > Thanks, > Amit > > > On Fri, Feb 19, 2010 at 2:27 PM, Mark Abraham wrot

Re: [gmx-users] domain decomposition and load balancing

Hi Mark, I am not using PME calculation. I was hoping mdrun will do the cell allocation itself. Thanks, Amit On Fri, Feb 19, 2010 at 2:27 PM, Mark Abraham wrote: > - Original Message - > From: Amit Choubey > Date: Saturday, February 20, 2010 8:51 > Subject: [gmx-users] domain decompo

Re: [gmx-users] domain decomposition and load balancing

- Original Message - From: Amit Choubey Date: Saturday, February 20, 2010 8:51 Subject: [gmx-users] domain decomposition and load balancing To: Discussion list for GROMACS users > Hi Everyone, > I am trying to run a simulation with the option "pbc=xy" turned on. I am > using 64 processo

Re: [gmx-users] domain decomposition errors

Thanks david: the chrash error is : Making 2D domain decomposition 4 x 2 x 1 starting mdrun 'PLASMEPSIN 2 in water' 3000 steps, 6.0 ps. Step 33, time 0.066 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1.084460, max 31.492893 (between atoms 3168 and 3169) bonds that r

Re: [gmx-users] domain decomposition errors

pedro alberto valiente flores wrote: Hi gromacs users: I' am trying to run a MD simulation of PlmII+Inhibitor system in cubic box (59002 atoms) with gromacs 4.0.5 on 8 processors, but my simulation crashes. In attach are files.tgz which contains the log (PlmII+PepstatinA_free.log) and error file

Re: [gmx-users] domain decomposition error

ot be possible. -Justin Regards, Nikhil *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Sun, 11 October, 2009 4:20:58 PM *Subject:* Re: [gmx-users] domain decomposition error nikhil damle wrote:

Re: [gmx-users] domain decomposition error

ikhil From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Sun, 11 October, 2009 4:20:58 PM Subject: Re: [gmx-users] domain decomposition error nikhil damle wrote: > Hi, > > I am trying to run a vacuum simulation of a system associated with ATP and &g

Re: [gmx-users] domain decomposition error

nikhil damle wrote: Hi, I am trying to run a vacuum simulation of a system associated with ATP and peptide. Being vacuum MD i removed pressure coupling and included plain electrostatic cut-offs while calculating potential. Energy minimisation converged to machine precesion even though not u