[gmx-users] Reverse micelle clustering issue
Tyler Cropley
tyler.cropley at wagner.edu
Wed Jul 22 21:19:32 CEST 2015
Thank you for your response! I used the code that you provided and my
micelle is now in the middle.
My mass ratio for isooctane is about 88% if you were still curious. Once
again thank you for your help.
Thank you,
Tyler Cropley
On Wed, Jul 22, 2015 at 4:57 AM, ABEL Stephane 175950 <Stephane.ABEL at cea.fr>
wrote:
> Hello
>
> To center your RM inside teh box you could use to successive trjconv
> commands with pbc cluster and mol
>
> in index.ndx
>
> 0 : all
> 1 AOT
> 2 water
> 3 AOT_Water
> 4 ISO
>
> 1 -- select 1 1 0 (or 2 2 0)
>
> echo 1 1 0 | trjconv -f my_initial.xtc -s my_tpr.tpr -pbc cluster -ur
> compact -center -o my_clustered,xtc
>
> 2 - 2 0 (or 1 0)
>
> echo 1 0 | trjconv -f my_clustered,xtc -s my_tpr.tpr -pbc mol -ur
> compact -center -o my_all_centered,xtc
>
> With these commands, the RM should be inside the box
>
> BTW;
>
> Your box is a bit too small for me, What is the isooctane mass fraction ?
>
> HTH
>
> Stephane
>
> ------------------------------
>
> Message: 3
> Date: Tue, 21 Jul 2015 17:38:30 -0300
> From: "V.V.Chaban" <vvchaban at gmail.com>
> To: gmx-users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Reverse micelle clustering issue
> Message-ID:
> <
> CAPXdD+aVsj3pkS0+cSYCatGP1TSod9B-rqjXbETk+aytsJJgNA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> The general advice to use trjconv with every keyword independently.
>
> In certain cases, its behavior is fairly bizarre if one uses all
> keywords at the same time. Probably, order of called procedures in the
> code matters...
>
>
> Professor Vitaly V. Chaban
>
>
>
>
> On Tue, Jul 21, 2015 at 3:08 PM, Tyler Cropley <tyler.cropley at wagner.edu>
> wrote:
> > Dear Gromacs users,
> >
> >
> > We ran a simulation of an AOT reverse micelle in isooctane solvent. We
> > followed instructions
> > http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering . For
> > clustering we selected the group that contains AOT and for output we
> > selected the entire system. The reverse micelle appears outside of the
> > solvent box in vmd. This is the picture
> >
> http://s24.photobucket.com/user/tycropley/media/RM-issue_zpsbngarszw.png.html
> > . We used -center and -boxcenter for trjconv but it did not work.
> >
> >
> > Is there a way to ensure that the corrected trajectory displays the
> > reverse micelle inside the solvent box? Or is there something more
> > seriously wrong?
> >
> >
> > Thank you,
> >
> > Tyler
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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> send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 21 Jul 2015 17:16:41 -0500
> From: Krzysztof Kuczera <kkuczera at ku.edu>
> To: <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] GROMACS 5.0.5 GPU version on K620
> Message-ID: <55AEC4C9.5070206 at ku.edu>
> Content-Type: text/plain; charset="utf-8"; format=flowed
>
> Hi Szil?rd ,
>
> The test case worked after I added the flags you recommended, though the
> speed was not as high as I had hoped - equivalent to about 6 CPU cores -
> I guess my GPU is not so hot.
>
> Below is the output from "mdrun -version". Please let me know if you
> see things that might be optimized there.
>
> Thanks for your excellent help!
>
> Krzysztof
> -------------------------------
> Gromacs version: VERSION 5.0.5
> Precision: single
> Memory model: 64 bit
> MPI library: thread_mpi
> OpenMP support: enabled GPU support: enabled invsqrt
> routine: gmx_software_invsqrt(x)
> SIMD instructions: AVX2_256
> FFT library: fftw-3.3.4-fma-sse2-avx RDTSCP usage: enabled C++11
> compilation: disabled TNG support: enabled
> Tracing support: disabled
> Built on: Tue Jul 21 16:25:29 CDT 2015
> Built by: kuczera at lolipop-chem-ku-edu [CMAKE]Build
> OS/arch: Linux 3.10.0-229.4.2.el7.x86_64 x86_64
> Build CPU vendor: GenuineIntel
> Build CPU brand: Intel(R) Xeon(R) CPU E5-2687W v3 @ 3.10GHzBuild CPU
> family: 6 Model: 63 Stepping: 2Build CPU features: aes apic avx
> avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm m
> mx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp
> sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apicC compiler: /usr/bin/cc GNU
> 4.8.3C compiler flags: -march=core-avx2 -Wno-maybe-uninitialized
> -Wextra -Wno-missing-field-initializers -Wno-sign-compare
> -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -O3
> -DNDEBUG -fomit-frame-pointer -funroll-all-
> loops -fexcess-precision=fast -Wno-array-bounds
> C++ compiler: /usr/bin/c++ GNU 4.8.3
> C++ compiler flags: -march=core-avx2 -Wextra
> -Wno-missing-field-initializers -Wpointer-arith -Wall
> -Wno-unused-function -O3 -DNDEBUG -fomit-frame-pointer
> -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds
> Boost version: 1.53.0 (external)
> CUDA compiler: /usr/local/cuda-7.0/bin/nvcc nvcc: NVIDIA (R) Cuda
> compiler driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on
> Mon_Feb_16_22:59:02_CST_2015;Cuda compilation tools, release 7.0, V7.0.27
> CUDA compiler
>
> flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_35,code=compute_35;-gencode;arch=compute_50,code=compute_50;-use_fast_math;-Xcompiler;-fPIC
> ;
>
> ;-march=core-avx2;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;-fomit-frame-pointer;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;
> CUDA driver: 7.0
> CUDA runtime: 7.0
>
>
> On 7/17/15 5:39 PM, Szil?rd P?ll wrote:
> > Krzysztof,
> >
> > Whyle GROMACS 5.0.x build system does not explicitly generate options
> > targeting 5.x devices, the binary built should still be compatible with
> > your GPU. You can try adding the device-specific optimization flags with
> the
> > -DCUDA_NVCC_FLAGS_RELEASE="-gencode;arch=compute_50,code=sm_50"
> > cmake flag, but I'm not sure this fix the issue.
> >
> > What does gmx -version show?
> >
> > Cheers,
> >
> > --
> > Szil?rd
> >
> > On Fri, Jul 17, 2015 at 11:49 PM, Krzysztof Kuczera <kkuczera at ku.edu>
> wrote:
> >
> >> Hi Group,
> >>
> >> I am getting a run-time error on my Linux workstation with K620 GPU
> >> for the GPU version of GROMACS 5.0.5
> >> using gcc 4.8.3 and CUDA Toolkit 7.0 I had no problem compiling the
> code
> >> but got this error when starting a test case:
> >>
> >> Program mdrun, VERSION 5.0.5
> >> Source code file:
> >> /home/kuczera/prog/gromacs-5.0.5/src/gromacs/mdlib/nbnxn_cuda/
> >> nbnxn_cuda.cu, line: 619
> >>
> >> Fatal error:
> >> cudaStreamSynchronize failed in cu_blockwait_nb: an illegal memory
> access
> >> was encountered
> >>
> >> Searching the Web, I found that this type of error was already resolved
> in
> >> GROMACS 4.6 some time ago.
> >> Could somebody suggest a solution?
> >>
> >> We have been able to compile and run GROMACS 5.0.4 on an older GPU with
> >> compute capability 3.5,
> >> my newer K620 has compute capability 5.0 - could this be the problem ?
> >>
> >> Thanks
> >> Krzysztof
> >>
> >> --
> >> Krzysztof Kuczera
> >> Departments of Chemistry and Molecular Biosciences
> >> The University of Kansas
> >> 1251 Wescoe Hall Drive, 5090 Malott Hall
> >> Lawrence, KS 66045
> >> Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu
> >> http://oolung.chem.ku.edu/~kuczera/home.html
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
>
>
> --
> Krzysztof Kuczera
> Departments of Chemistry and Molecular Biosciences
> The University of Kansas
> 1251 Wescoe Hall Drive, 5090 Malott Hall
> Lawrence, KS 66045
> Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu
> http://oolung.chem.ku.edu/~kuczera/home.html
>
>
>
> ------------------------------
>
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