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-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > 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 <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Regarding structure analysis of DNA > Message-ID: <53148e5b.8010...@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 > > jalem...@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 <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Set the environment variables of > "FFTW3_INCLUDE_DIR" and "FFTW3_LIBRARIES" > Message-ID: <53148ed5.2050...@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 > > jalem...@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 <jolayfi...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Two-body Bonded Distance > Message-ID: <1393856804341-5014891.p...@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 <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Question about Improper Dihedral of Charmm in > gmx & ParamChem > Message-ID: <53149149.6080...@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 > > jalem...@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 <writetoas...@gmail.com> > To: gmx-us...@gromacs.org > Subject: [gmx-users] md_pull code in umbrella sampling > Message-ID: > < > cam90emycoyzvjvw4z7xuagsxwkl1y0y26bn4exaxgmzv_hs...@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 <gromacsqu...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Subject: [gmx-users] No default U-B types charmm > Message-ID: > < > cape3fjaqeu8vb9ymmhin3srwzdaqtbqbatesmwqrcxwg9fg...@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 > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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