thanks for confirming.
best regards
On Wed, Oct 21, 2020 at 4:08 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> The --nprocs argument will come into play only if you're using CPU
> code for MD or minimization (i.e. pmemd.MPI or sander.MPI). The
> analysis is super quick and so is always done in serial. Using the cpu
> code may be desirable in some cases where extremely large forces are
> encountered, but in general I've found that the DP GPU code does a
> good job for minimization.
>
> So as long as you're using the GPU for both MD and minimization,
> --nprocs has no effect. Hope this helps,
>
> -Dan
>
> On Sat, Oct 10, 2020 at 12:05 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
> >
> > Dear Daniel,
> > I have used this tool for 4-5 structures now and didn't encounter any
> obvious errors or problems.
> >
> > I have another question though, related to the option --nprocs.
> > Since most of the min and MD jobs are run on the GPU with pmemd.cuda,
> I'm assuming that the script assigns these CPUs only for the analysis
> performed by cpptraj (github/AmberTools version).
> > Nonetheless, I observed that only 1 CPU is used even if I assign > 4
> (default) values.
> > I'm just trying to understand how to figure out the optimum usage
> (CPU/GPU) in case I need to run this script for a significant number of
> structures.
> > Can you please find time to suggest on this aspect?
> >
> > Looking forward to your valuable suggestions.
> > Thank you and best regards
> > Vaibhav
> >
> > On Thu, Oct 1, 2020 at 1:00 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
> >>
> >> Dear Daniel,
> >> One small-thing I already noticed that it was necessary to use the
> --ares argument twice to specify two different non-standard residues which
> I wanted to restrain in the initial steps.
> >> That is --ares HM1 FE1 failed to apply restraints on the 2nd residue in
> the md input files.
> >> But using it like the following worked.
> >> --ares HM1 --ares FE1
> >>
> >> I hope this helps optimize the usage of different options in the next
> update/release.
> >> Please let me know if you want any other specific detail that might add
> value.
> >> Best regards
> >>
> >>
> >> On Wed, Sep 30, 2020 at 7:23 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
> >>>
> >>> It was my impatience, I forgot to make install.
> >>> Afterwards I can't find any obvious error.
> >>> I will have a closer look tomorrow at all steps and let you know if I
> have any questions.
> >>> Thanks for making such a valuable tool.
> >>>
> >>>
> >>> On Wed, Sep 30, 2020, 19:05 Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >>>>
> >>>> Hi,
> >>>>
> >>>> If possible, could you say exactly what the problem was so that other
> >>>> people who might encounter this can fix it (and so if it's an issue
> >>>> with the script I can fix it). Also, since the script is very much a
> >>>> beta version, any other feedback (negative or positive) is much
> >>>> appreciated.
> >>>>
> >>>> -Dan
> >>>>
> >>>> On Wed, Sep 30, 2020 at 7:54 AM Vaibhav Dixit <
> vaibhavadixit.gmail.com> wrote:
> >>>> >
> >>>> > FYI, I'm now able to fix the installation issue and will get back
> to you if I any further questions on analyzing the data.
> >>>> > thank you.
> >>>> >
> >>>> > On Wed, Sep 30, 2020 at 12:19 PM Vaibhav Dixit <
> vaibhavadixit.gmail.com> wrote:
> >>>> >>
> >>>> >> Dear Daniel and Amber community,
> >>>> >> I'm trying to use the AmberMdPrep script to equilibrate a
> protein+non-standard residue.
> >>>> >> As recommended, I have first installed the github version of
> cpptraj and sourced it (as suggested at the end of the installation).
> >>>> >> The AmberMdPrep script seems to be working well, but in the last
> step it is unable to pick the right installation of cpptraj as shown below.
> >>>> >> Can you please suggest me how to fix this and make the script use
> the correct cpptraj version?
> >>>> >> Thank you and best regards.
> >>>> >>
> >>>> >> (base) [exx.c107739 test-AmberMDprep]$ source
> /home/exx/Downloads/cpptraj-master/cpptraj.sh
> >>>> >> (base) [exx.c107739 test-AmberMDprep]$ AmberMDPrep -p
> ../1HGA_solv.prmtop -c ../1HGA_solv.inpcrd --ares HM1 --ares FE1 -O --temp
> 310
> >>>> >> AmberMdPrep.sh Version 0.2 (beta)
> >>>> >> 140 protein, 0 dna, 0 rna, 0 lipid, 0 carbohydrate, 6302 water,
> 4 other
> >>>> >> Unknown residues names: Cl-,FE1,HD1,HM1
> >>>> >> Detected additional res mask: :FE1,HM1&!.H=
> >>>> >> Warning: Unknown residues detected; will be ignored for restraints.
> >>>> >> Detected types : protein
> >>>> >> Orthogonal box detected.
> >>>> >> TOP : ../1HGA_solv.prmtop
> >>>> >> CRD : ../1HGA_solv.inpcrd
> >>>> >> NUM SOLUTE RES : 140
> >>>> >> HEAVY MASK : :1-140&!.H=
> >>>> >> BACKBONE MASK : :1-140.H,N,CA,HA,C,O
> >>>> >> ADDITIONALMASK : :FE1,HM1&!.H=
> >>>> >> ADD. MASK RES. : HM1 FE1
> >>>> >> TEMPERATURE : 310
> >>>> >> OVERWRITE : 1
> >>>> >> MD COMMAND : pmemd.cuda
> >>>> >> MIN COMMAND : pmemd.cuda_DPFP
> >>>> >> NPROCS : 4
> >>>> >>
> >>>> >> Performing standard min/equil
> >>>> >> Minimization: step1
> >>>> >> MD: step2
> >>>> >> Minimization: step3
> >>>> >> Minimization: step4
> >>>> >> Minimization: step5
> >>>> >> MD: step6
> >>>> >> MD: step7
> >>>> >> MD: step8
> >>>> >> MD: step9
> >>>> >> Starting final density equilibration.
> >>>> >> /usr/local/amber18/bin/cpptraj does not support density plateau
> evaluation.
> >>>> >> Only running one round of final density equilibration.
> >>>> >> Final 1
> >>>> >> MD: final.1
> >>>> >> Skipping final density evaluation.
> >>>> >> Complete.
> >>>> >> Equilibration success
> >>>> >>
> >>>> >>
> >>>> >> (base) [exx.c107739 cpptraj-master]$ ./configure -amberlib gnu
> >>>> >>
> >>>> >> Testing C++ compiler: OK
> >>>> >> Testing C compiler: OK
> >>>> >> Testing Fortran compiler: OK
> >>>> >> Testing basic C++11 support: OK
> >>>> >> Testing system headers for C++11 support: OK
> >>>> >> Using blas from /usr/local/amber18
> >>>> >> Using lapack from /usr/local/amber18
> >>>> >> Using netcdf from /usr/local/amber18
> >>>> >> Checking BZLIB: OK
> >>>> >> Checking ZLIB: OK
> >>>> >> Checking NetCDF: OK
> >>>> >> Checking LAPACK/BLAS: OK
> >>>> >> Checking for FFTW3 from AMBERHOME: OK
> >>>> >> Checking for sanderlib: OK
> >>>> >>
> >>>> >> Configuration summary:
> >>>> >> Build type: Serial
> >>>> >> Options: netcdf bzlib tng zlib arpack lapack blas fftw3 readline
> xdrfile sanderlib
> >>>> >> Target platform: Linux, 64-bit.
> >>>> >> gnu compilers in use.
> >>>> >> C++11 support enabled.
> >>>> >> PME support enabled.
> >>>> >> Compiler optimizations are on.
> >>>> >>
> >>>> >> Cleaning source directory.
> >>>> >>
> >>>> >>
> --------------------------------------------------------------------------------
> >>>> >> An environment resource file for CPPTRAJ has been created:
> >>>> >> /home/exx/Downloads/cpptraj-master/cpptraj.sh
> >>>> >> You may 'source' this file to set up your environment for CPPTRAJ.
> >>>> >>
> --------------------------------------------------------------------------------
> >>>> >>
> >>>> >> CPPTRAJ configuration complete.
> >>>> >>
> >>>> >>
> >>>> >> --
> >>>> >>
> >>>> >> Regards,
> >>>> >>
> >>>> >> Dr. Vaibhav A. Dixit,
> >>>> >>
> >>>> >> Visiting Scientist at the Manchester Institute of Biotechnology
> (MIB), The University of Manchester, 131 Princess Street, Manchester M1
> 7DN, UK.
> >>>> >>
> >>>> >> AND
> >>>> >> Assistant Professor,
> >>>> >> Department of Pharmacy,
> >>>> >> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> >>>> >> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> >>>> >> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> >>>> >> India.
> >>>> >> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> >>>> >> Email: vaibhav.dixit.pilani.bits-pilani.ac.in,
> vaibhavadixit.gmail.com
> >>>> >> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> >>>> >> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> >>>> >>
> >>>> >> ORCID ID: https://orcid.org/0000-0003-4015-2941
> >>>> >>
> >>>> >>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >>>> >>
> >>>> >> P Please consider the environment before printing this e-mail
> >>>> >>
> >>>> >
> >>>> >
> >>>> > --
> >>>> >
> >>>> > Regards,
> >>>> >
> >>>> > Dr. Vaibhav A. Dixit,
> >>>> >
> >>>> > Visiting Scientist at the Manchester Institute of Biotechnology
> (MIB), The University of Manchester, 131 Princess Street, Manchester M1
> 7DN, UK.
> >>>> >
> >>>> > AND
> >>>> > Assistant Professor,
> >>>> > Department of Pharmacy,
> >>>> > ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> >>>> > Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> >>>> > VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> >>>> > India.
> >>>> > Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> >>>> > Email: vaibhav.dixit.pilani.bits-pilani.ac.in,
> vaibhavadixit.gmail.com
> >>>> > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> >>>> > https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> >>>> >
> >>>> > ORCID ID: https://orcid.org/0000-0003-4015-2941
> >>>> >
> >>>> >
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >>>> >
> >>>> > P Please consider the environment before printing this e-mail
> >>>> >
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >>
> >> Regards,
> >>
> >> Dr. Vaibhav A. Dixit,
> >>
> >> Visiting Scientist at the Manchester Institute of Biotechnology (MIB),
> The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> >>
> >> AND
> >> Assistant Professor,
> >> Department of Pharmacy,
> >> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> >> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> >> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> >> India.
> >> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> >> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> >> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> >> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> >>
> >> ORCID ID: https://orcid.org/0000-0003-4015-2941
> >>
> >> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >>
> >> P Please consider the environment before printing this e-mail
> >>
> >
> >
> > --
> >
> > Regards,
> >
> > Dr. Vaibhav A. Dixit,
> >
> > Visiting Scientist at the Manchester Institute of Biotechnology (MIB),
> The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> >
> > AND
> > Assistant Professor,
> > Department of Pharmacy,
> > ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> > Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> > VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> > India.
> > Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> > Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> > http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> > https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
> >
> > ORCID ID: https://orcid.org/0000-0003-4015-2941
> >
> > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >
> > P Please consider the environment before printing this e-mail
> >
>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
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Received on Wed Oct 21 2020 - 05:00:03 PDT
