[gmx-users] gromacs.org_gmx-users Digest, Vol 119, Issue 10
Tom
dnaafm at gmail.com
Tue Mar 4 05:03:07 CET 2014
Thanks Justin!
The result about the improper dihedral angle from ParamChem does keep
me very confused. For the molecule (C6H5-NH2), the one of N H H C should
not have improper dihedral however the websever showes there is one.
If anyone has the experience of Charmm improper dihedral, please give a
help. Thanks!
Thom
On Mon, Mar 3, 2014 at 9:57 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: Regarding structure analysis of DNA (Justin Lemkul)
> 2. Re: Set the environment variables of "FFTW3_INCLUDE_DIR" and
> "FFTW3_LIBRARIES" (Justin Lemkul)
> 3. Re: Two-body Bonded Distance (jolayfield)
> 4. Re: Question about Improper Dihedral of Charmm in gmx &
> ParamChem (Justin Lemkul)
> 5. md_pull code in umbrella sampling (Arunima Shilpi)
> 6. No default U-B types charmm (gromacs query)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 03 Mar 2014 09:14:51 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Regarding structure analysis of DNA
> Message-ID: <53148E5B.8010402 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 3/3/14, 4:05 AM, Sathish Kumar wrote:
> > Hai
> > I have done simulation of DNA on carbon nano tube surface. I
> want
> > to calculate structural changes (means changes in stacking, puckering
> > angles and bending of helix) in DNA. Can any suggest me how to calculate
> > these things.
> >
>
> Chapter 8 describes all available analysis tools. For more complicated
> things,
> you may need outside software like MDAnalysis or similar packages.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 03 Mar 2014 09:16:53 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Set the environment variables of
> "FFTW3_INCLUDE_DIR" and "FFTW3_LIBRARIES"
> Message-ID: <53148ED5.2050804 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 3/3/14, 5:26 AM, Hassan Aaryapour wrote:
> > Dear Gmx-user;
> > I want to install double precision gromacs 4.5.3 and FFTW 3.3.2 in my
> > home directory.
> > first, according to the FFTW installation instructions I installed and
> > introduced it to bash shell it as the following order:
> >
> > $tar -xzvf fftw-3.3.2.tar.gz
> > $./configure --enable-threads --prefix=/home/WeNMR/ProgramFiles/fftw
> > $make
> > $make install
> >
> > export CPPFLAGS=-I/home/WeNMR/ProgramFiles/fftw/include
> > export LDFLAGS=-L/home/WeNMR/ProgramFiles/fftw/lib
> >
> > but it isn't found automatically by cmake when I want to install gromacs.
> > and this error was appeared:
> >
> > CMake Error at
> >
> /usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108
> > (message):
> > Could not find FFTW3. Provide the fftw3 install directory in the
> > FFTW3_ROOT_DIR environment variable. (missing: FFTW3_LIBRARIES
> > FFTW3_INCLUDE_DIR)
> > Call Stack (most recent call first):
> >
> /usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:315
> > (_FPHSA_FAILURE_MESSAGE)
> > cmake/FindFFTW3.cmake:31 (find_package_handle_standard_args)
> > CMakeLists.txt:636 (find_package)
> >
> >
> > How can I set the environment variables for "FFTW3_INCLUDE_DIR" and
> > "FFTW3_LIBRARIES"?
>
> Those are CMake command-line options. See the full installation
> instructions
> online, specifically
>
> http://www.gromacs.org/Documentation/Installation_Instructions#4.4._Helping_CMake_find_the_right_libraries.2fheaders.2fprograms
>
> Is there any reason you are installing outdated versions of Gromacs and
> FFTW?
>
> -Justin
>
> > can I add my FFTW installed path to "CMakeLists.txt" file in the
> > related section in below? how?
> >
> > if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
> > # MESSAGE(STATUS "Using external FFT library - fftw3")
> > if(GMX_DOUBLE)
> > find_package(FFTW3 REQUIRED)
> > include_directories(${FFTW3_INCLUDE_DIR})
> > set(FFT_LIBRARIES ${FFTW3_LIBRARIES})
> > set(PKG_FFT "fftw3")
> > else(GMX_DOUBLE)
> > find_package(FFTW3F REQUIRED)
> > include_directories(${FFTW3F_INCLUDE_DIR})
> > set(FFT_LIBRARIES ${FFTW3F_LIBRARIES})
> > set(PKG_FFT "fftw3f")
> > endif(GMX_DOUBLE)
> >
> >
> > Thank you in advance
> > Hassan
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 3 Mar 2014 06:26:44 -0800 (PST)
> From: jolayfield <jolayfield at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Two-body Bonded Distance
> Message-ID: <1393856804341-5014891.post at n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Justin,
>
> The two-body distance is about 4x the actual distance in the structure
> file. This spuriously large distance only appears once I add the virtual
> particle. This appears to not affect the actual MD run based on my tests
> with and without the virtual particle, but it does limit the number of
> processors that I am able to use during the run. Is there a reason that
> the
> distance should be different for the two-body bonded and multi-body bonded
> distance when they span the same atoms?
>
> Thanks,
>
> Josh
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Two-body-Bonded-Distance-tp5014864p5014891.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 03 Mar 2014 09:27:21 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Question about Improper Dihedral of Charmm in
> gmx & ParamChem
> Message-ID: <53149149.6080902 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 3/3/14, 12:27 AM, Tom wrote:
> > Dear Gromacs Users,
> >
> > I am confused about the definition of improper dihedral angle of Charmm
> > used in gromacs.
> >
> > I used two molecle
> > 1)M1: C6H5-NH2
> > 2)MP1: C6H5-NH-C=O
> > |
> > CH3
> > After I submitted to the webserver of ParamChem, the output str files in
> > the attachment show that
> >
> > *For M1*, IMPROPERS
> >
> > NG2S3 HGP4 HGP4 CG2R61 -2.5000 0 0.00 ! -2.0 PYRIDINE
> > aminopyridine 11/10 kevo: sic! Compensates for in-plane force from
> > CG2R61 CG2R61 NG2S3 HGP4
> >
> > *For MP1*, IMPROPERS
> > CG2O1 CG331 NG2S1 OG2D1 120.0000 0 0.00 ! PROT NMA Vibrational Modes (LK)
> > WILDCARD
> >
> > For M1, with a NH2 group, ParamChem gives an improper dihedral *with N
> as a
> > central atom*.
> >
> > However, for MP1, with a NH1 internal group, ParamChem does not give any
> > dihedrals *with N as a central atom*.
> >
>
> It shouldn't. The CHARMM force field uses few improper dihedrals in
> general,
> and there are none around N in acetamides. See examples in model
> compounds like
> NMA, DMA, etc in the CHARMM force fields.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 3 Mar 2014 20:04:09 +0530
> From: Arunima Shilpi <writetoash28 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] md_pull code in umbrella sampling
> Message-ID:
> <
> CAM90emYcoyZVjVW4Z7xuagSxwKL1y0Y26Bn4EXAxgmZv_hSArw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Sir
>
> I am trying to calculate the potential mean force (PMF) between protein
> and Ligand. I have applied position restrain to protein. I have applied
> reference pulling group to Protein and Pulling force has been applied to
> ligand. The pul force is applied along Z-axis. I had query as to whether I
> am proceeding in the right direction. Here I have provided the detail of
> the content of md_pull.mdp
>
> md_pull.mdp
>
> title = Umbrella pulling simulation
> define = -DPOSRES_Protein
> ; Run parameters
> integrator = md
> dt = 0.002
> tinit = 0
> nsteps = 250000 ; 500 ps
> nstcomm = 10
> ; Output parameters
> nstxout = 5000 ; every 10 ps
> nstvout = 5000
> nstfout = 500
> nstxtcout = 500 ; every 1 ps
> nstenergy = 500
> ; Bond parameters
> constraint_algorithm = lincs
> constraints = all-bonds
> continuation = yes ; continuing from NPT
> ; Single-range cutoff scheme
> nstlist = 5
> ns_type = grid
> rlist = 1.4
> rcoulomb = 1.4
> rvdw = 1.4
> ; PME electrostatics parameters
> coulombtype = PME
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = Nose-Hoover
> tc_grps = Protein Non-Protein
> tau_t = 0.5 0.5
> ref_t = 310 310
> ; Pressure coupling is on
> Pcoupl = Parrinello-Rahman
> pcoupltype = isotropic
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
> refcoord_scaling = com
> ; Generate velocities is off
> gen_vel = no
> ; Periodic boundary conditions are on in all directions
> pbc = xyz
> ; Long-range dispersion correction
> DispCorr = EnerPres
> ; Pull code
> pull = umbrella
> pull_geometry = distance ; simple distance increase
> pull_dim = N N Y
> pull_start = yes ; define initial COM distance > 0
> pull_ngroups = 1
> pull_group0 = Protein
> pull_group1 = DRG
> pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns
> pull_k1 = 1000 ; kJ mol^-1 nm^-2
>
> Regards
>
>
> Arunima
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 3 Mar 2014 15:57:55 +0000
> From: gromacs query <gromacsquery at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: [gmx-users] No default U-B types charmm
> Message-ID:
> <
> CAPe3FJAqEu8vb9YMmhin3srwZDAQTbqbatESmwqRcxwG9FGTjg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi All
>
> I am trying to use charmm36 (charmm36-jan2014 from charmm website) with
> popc membrane built using charmm-gui (have water and ions).
>
> I used commands as follows:
>
> pdb2gmx -f step5_assembly.pdb -o popc.gro -water tip3p -ff charmm36-jan2014
> editconf -f popc.gro -o popc_box.gro -c -d 0.0
> grompp -f minim.mdp -c popc_box.gro -p topol.top -o em.tpr
>
> I get this error: (so many)
> ERROR 11520 [file topol.top, line 184419]:
> No default U-B types
>
> Where are UB for charmm36?
>
> thanks,
> JIom
>
>
> ------------------------------
>
> --
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> End of gromacs.org_gmx-users Digest, Vol 119, Issue 10
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