[gmx-users] The simulation of big protein in implicit solvent

[Yi Isaac Yang]

Thank you very much! But I just perform the minimization in my own computer:

yangy at magadino:/mnt/storage2/yangy/l_repressor$ gmx mdrun -v -deffnm
lrepressor_min

                   :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:

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GROMACS:      gmx mdrun, VERSION 5.1.2
Executable:   /home/yangy/opt/bin/gmx
Data prefix:  /home/yangy/opt
Command line:
  gmx mdrun -v -deffnm lrepressor_min


Running on 1 node with total 4 cores, 8 logical cores
Hardware detected:
  CPU info:
    Vendor: GenuineIntel
    Brand:  Intel(R) Xeon(R) CPU E3-1246 v3 @ 3.50GHz
    SIMD instructions most likely to fit this hardware: AVX2_256
    SIMD instructions selected at GROMACS compile time: AVX2_256

Reading file lrepressor_min.tpr, VERSION 5.1.2 (single precision)

-------------------------------------------------------
Program gmx mdrun, VERSION 5.1.2
Source code file:
/home/yangy/Downloads/gromacs-5.1.2-patched/src/gromacs/domdec/domdec.cpp,
line: 6542

Fatal error:
Domain decomposition does not support simple neighbor searching, use grid
searching or run with one MPI rank
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------


In fact, I'm not very familiar with gromacs, before that I always use
AMBER. So could you tell me how to perform mdrun with "one MPI rank"?
Although I directly run it in my own computer, it still show that "Running
on 1 node with total 4 cores, 8 logical cores". And what is "domain
decomposition"? Could I change it? Although I can perform the minimization
in serial mode,  I must using MPI to perform the MD simulation.

Thank you very much and best regards,
Isaac

2016-09-01 15:08 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 9/1/16 5:49 AM, Yi Isaac Yang wrote:
>
>> Dear all,
>>
>> Recently, I want to simulate a big protein (about 90 residues) in GBSA
>> implicit
>> solvent using gromacs 5.1.2. However, when I want to perform the
>> minimization,
>> the program shows that:
>>
>> _Fatal error:__
>> __Domain decomposition does not support simple neighbor searching, use
>> grid
>> searching or run with one MPI rank__
>> __For more information and tips for troubleshooting, please check the
>> GROMACS__
>> __website at http://www.gromacs.org/Documentation/Errors_
>>
>> And the strange thing is, I can use the mdp file to minimization a small
>> protein
>> (6 residues, using the same force field), every thing is OK.
>>
>> If I delete "ns-type=simple" in mdp file, the minimization of  small
>> protein is
>> still OK. And the minimization of big protein is still not work:
>> _
>> __Fatal error:__
>> __Domain decomposition does not work with nstlist=0__
>> __For more information and tips for troubleshooting, please check the
>> GROMACS__
>> __website at http://www.gromacs.org/Documentation/Errors_
>>
>> As no-cutoff is needed in this simulation, I can't delete "_nstlist=0_".
>>
>> So you know how to solve this problem?
>>
>>
> Basically, you can't parallelize via DD.  See the other thread to which I
> just posted a reply.  Implicit simulations don't scale well and you are
> therefore limited in the types of algorithms that are supported.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Yesterday Young
College of Chemistry and Molecular Engineering
Peking University