[gmx-users] 回覆︰ 回覆︰ Simulations with SWM4-DP water model in non PBC

[Chi Yuen Pak]

Dear Prof. van der Spoel,
I have followed your suggestion and used the following commands with thread-MPI enabled "gmx" in GROMACS 2018.2:
gmx grompp -f eq.mdp -c em.gro -p swm4-dp.top -r posre.gro -o eq.tprmpirun -np 1 gmx mdrun -deffnm eq -ntomp 1 -ntmpi 2
then this gives me the following error message: -------------------------------------------------------
Fatalerror: Shellparticles are not implemented with domain decomposition, use a single rank 

-------------------------------------------------------
It seems to me that if multiple threads of thread-MPI are set, GROMACS will automatically turn on domain decomposition, which is not compatible with the simulations of shell particles (e.g. SWM4-DP water model). In this case, is it possible to carry out nonPBC simulations with SWM4-DP polarizable water model using multiple cores in GROMACS 2018.2?
The mdp, topology, and log file are linked at the end for your reference.
Thanks again for your help.

Best,Chi Yuen

mdp:https://www.dropbox.com/s/xq6s63x4j30hl1h/eq.mdp.pdf?dl=0topology:https://www.dropbox.com/s/0gj8ot2m6k8b019/swm4-dp.top.pdf?dl=0logfile: https://www.dropbox.com/s/o5frxpr7jwfqita/eq-gmx-2ntmpi.pdf?dl=0



 

    David van der Spoel <spoel at xray.bmc.uu.se> 於 2018年08月14日 (週二) 4:11 AM 寫道﹕
 

 Den 2018-08-13 kl. 11:49, skrev Chi Yuen Pak:
> Dear Prof. van der Spoel,
> 
> 
> Thanks for your reply. I tried touse the following commands (2 OpenMP threads):
> 
> 
>  
> gmx_mpi grompp -f eq.mdp -c em.gro-p swm4-dp.top -r posre.gro -o eq.tpr
> 
> mpirun -np 1 gmx_mpi mdrun -ntomp 2-deffnm eq
> 
Did you try with thread-mpi?

mpirun -np 1 gmx_mpi mdrun -ntomp 1 -ntmpi 2


> 
>  
> but this gave me the following errormessage in GROMACS 2018.2:
> 
> -------------------------------------------------------
> 
> Fatal error:
> 
> OpenMP threads have been requestedwith cut-off scheme Group, but these are only supported with cut-off schemeVerlet
> 
> --------------------------------------------------------
> 
> 
>  
> I can successfully runthe simulation only when I set “–ntomp 1” with “Group” in nonPBC (since “Verlet” as the cutoff scheme is only supported in full PBC or pbc=xy)
> 
> 
>  
> The mdp, topology, and logfiles are linked at the end for your reference.
> 
> 
>  
> In addition, I have alsotried –pd option with GROMACS 4.6.7, but as far as I know, particledecomposition has not been supported since GROMACS 5.0.
> 
> 
>  
> There is another problemwith version 4.6. It seems that the flat-bottom restraint is also not supportedbefore version 5. It was reported that an error message would appear ifflat-bottom restraint was used in the version before GROMACS 5.0 (Ref.: https://redmine.gromacs.org/issues/1794). Therefore, may I ask how you carried out thesimulations with flat-bottom restraints in GROAMCS 4.6 in your 2011 paper?
> 
I guess we implemented the flat-bottom restraints in 4.6.7 but it was 
only included in grmoacs from 5.0.

> 
>  
> Thanks again for yourhelp.
> 
> 
>  
> 
>  
> Best,
> 
> Chi Yuen
> 
> 
>  
> 
>  
> mdp:https://www.dropbox.com/s/xq6s63x4j30hl1h/eq.mdp.pdf?dl=0
> 
> 
>  
> topology:https://www.dropbox.com/s/0gj8ot2m6k8b019/swm4-dp.top.pdf?dl=0
> 
> 
>  
> logfile when setting –ntomp to be 1: https://www.dropbox.com/s/p2pi2yvoo9x4d39/eq-1ntomp.log.pdf?dl=0
> 
> 
>  
> log file when setting –ntomp to be 2: https://www.dropbox.com/s/zn2pqr6qnrf192f/eq-2ntomp.log.pdf?dl=0
> 
> 
> 
> 
> 
> 
>  
> 
> 
> 
> |  | Virus-free. www.avast.com  |
> 
>      David van der Spoel <spoel at xray.bmc.uu.se> 於 2018年08月12日 (週日) 2:36 PM 寫道﹕
>  
> 
>  Den 2018-08-11 kl. 16:33, skrev Chi Yuen Pak:
>> Dear GROMACS users,
>>
>> I would like to ask a question concerning about the simulation of a water droplet, with SWM4-DP polarizable water model in nonperiodic boundary conditions. The GROMACS version I use is 2018.2. I have been only able to successfully run the simulation with only “Group” as the cutoff scheme in non PBC.  Multiple OpenMP threads are not supported with “Group”. Also, shell particles are not implemented with domain decomposition, so I have not been able to run the simulation with more than a single core. The following commands are what I use (with thread-MPI)gmx_mpi grompp -f eq.mdp -c em.gro -p swm4-dp.top -r posre.gro -o eq.tprmpirun -np 1 gmx_mpi mdrun -ntomp 1 -deffnm eq
> 
> Are you sure it is not using more than one thread? What does it say in
> the log file?
> 
>> In the paper “Atomistic simulation of ion solvation in water explains surface preference of halides” by Prof. David Van der Spoel in 2011 (doi: 10.1073/pnas.1017903108), they also used the SWM4-DP water model in non PBC (no cutoffs) in GROMACS. I can only guess they used multiple cores for their simulations, or did they? Does anyone know if it is possible to run multiple cores to simulate SWM4-DP in non PBC?
> That was run with gromacs 4.6 using the -pd option.
> You could do that as well of course.
>>
>> Attached are the mdp setting and topology for your reference.Thanks.
>> Best,Chi Yuen
>> mdp setting:  https://www.dropbox.com/s/e1sord21slgn084/eq.mdp.pdf?dl=0
>>
>> topology: https://www.dropbox.com/s/0gj8ot2m6k8b019/swm4-dp.top.pdf?dl=0
>>
>> |  | Virus-free. www.avast.com  |
>>
> 
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
-- 
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