Hi everyone I'm going to run md simulation but when i use grompp command i face this warning:
WARNING 1 [file "DRGGMX.ITP", line 18]: > Too few parameters on line (source file toppush.c, line 731) can everyone help me please? On Mon, Jun 8, 2015 at 2:18 PM, < [email protected]> wrote: > Send gromacs.org_gmx-users mailing list submissions to > [email protected] > > 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 > [email protected] > > You can reach the person managing the list at > [email protected] > > 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: Problems installing gromacs 5.0.4 with plumed 2.1.2 for > MPI ([email protected]) > 2. Re: Microwave (Mostafa Javaheri) > 3. gmx distance (Poncho Arvayo Zatarain) > 4. cudaStreamSynchronize failed in cu_blockwait_nb (Alex) > 5. Re: cudaStreamSynchronize failed in cu_blockwait_nb (Alex) > 6. Immediate PhD Opening In Computational Structural Biology Of > Membrane Proteins (Marawan Hussien) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 8 Jun 2015 18:57:37 +0100 > From: [email protected] > To: "James Krieger" <[email protected]> > Cc: gmx users-list <[email protected]> > Subject: Re: [gmx-users] Problems installing gromacs 5.0.4 with plumed > 2.1.2 for MPI > Message-ID: > <[email protected]> > Content-Type: text/plain > > More details are available on the plumed forum google group at > > https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/plumed-users/stlK9-kaa6A/jSm8rOON_xsJ > > > Hi, > > > > I have successfully installed plumed-2.1.2 (I believe with MPI > > capabilities) and patched it onto gromacs-5.0.4, I am now trying to > > install the gromacs and it's not working. Here are my errors from make: > > > > collect2: error: ld returned 1 exit status > > src/gromacs/CMakeFiles/libgromacs.dir/build.make:22956: recipe for target > > 'lib/libgromacs_mpi.so.0.0.0' failed > > make[2]: *** [lib/libgromacs_mpi.so.0.0.0] Error 1 > > CMakeFiles/Makefile2:1948: recipe for target > > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed > > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 > > Makefile:146: recipe for target 'all' failed > > make: *** [all] Error 2 > > > > I have successfully installed the latest gcc compilers and tried to tell > > gromacs to use them with the following command (not sure if this is > > right): > > ccmake ../gromacs-5.0.4/ -DGMX_BUILD_OWN_FFTW=ON > > -DCMAKE_C_COMPILER=/lmb/home/jkrieger/bin/gcc-5.1.0-build/bin/gcc > > > > In any case I get similar errors using the default compilers on my > system. > > > > I am installing on a front-end node of our cluster at the LMB, which has > a > > shared filesystem. > > > > Please let me know if there's anything else I need to tell you so that > you > > can help. > > > > Many thanks > > James > > > > > > > ------------------------------ > > Message: 2 > Date: Mon, 8 Jun 2015 22:34:02 +0430 > From: Mostafa Javaheri <[email protected]> > To: [email protected] > Subject: Re: [gmx-users] Microwave > Message-ID: > <CAH0JJJKJdmfYA=Yvt= > [email protected]> > Content-Type: text/plain; charset=UTF-8 > > Dear Mark, > > The authors didn't circulate the modified version of GROMACS and they > couldn't be able for any help. It would be very kind of you if you could > give me some information about which file or files of the source code > should I alter for achieving this purpose. > > Best, > > Mostafa > > On Mon, Jun 8, 2015 at 8:05 AM, Mark Abraham <[email protected]> > wrote: > > > Hi, > > > > You'd have to contact the authors to get their modified version. > > > > Mark > > > > On Sun, Jun 7, 2015 at 11:09 PM Mostafa Javaheri < > > [email protected]> > > wrote: > > > > > Hi all, > > > > > > Thanks for your replies, > > > > > > I searched about the simulation under e/m field and as far as I > > understood, > > > I have to alter the source code for that, but I don't know how to do > this > > > and which part of the source code must change exactly. several studies > > have > > > been performed by Niall J. English and co ( > > > > http://scitation.aip.org/content/aip/journal/jcp/131/3/10.1063/1.3184794 > > ) > > > and (http://adsabs.harvard.edu/abs/2003JChPh.118.1589E) which I'm > > tending > > > to do the same but with different protein, due to the correspondence, > > they > > > used modified version of GROMACS 3 in their studies. > > > I would be thankful if you could give me some idea about this kind of > > > modification? > > > > > > Best, > > > > > > Mostafa > > > > > > On Tue, Jun 2, 2015 at 4:37 PM, Justin Lemkul <[email protected]> wrote: > > > > > > > > > > > > > > > On 6/2/15 4:31 AM, Mostafa Javaheri wrote: > > > > > > > >> Dear Justin, > > > >> > > > >> How could I simulate a membrane protein while there is microwave > > > >> radiations in > > > >> one direction e.g. in direction of z-axis? Should I change the > > > >> delta-lambda > > > >> > > > > > > > > delta-lambda is a free energy option. > > > > > > > > or Is this accessible via electric field option? If I have to use > > > electric > > > >> field option, should I patch the mdrun ( > > > >> > > http://www.gromacs.org/Developer_Zone/Programming_Guide/Patching_mdrun > > > )? > > > >> > > > >> > > > > Electric fields are already supported, but I don't think this is > > > > physically what you want. I have no idea how to microwave an MD > > > simulation. > > > > > > > > -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 > > > > > > > > [email protected] | (410) 706-7441 > > > > http://mackerell.umaryland.edu/~jalemkul > > > > > > > > ================================================== > > > > -- > > > > 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 > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to [email protected]. > > > > > > > -- > > > 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 > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to [email protected]. > > > > > -- > > 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 > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to [email protected]. > > > > > ------------------------------ > > Message: 3 > Date: Mon, 8 Jun 2015 15:35:47 -0300 > From: Poncho Arvayo Zatarain <[email protected]> > To: "[email protected]" > <[email protected]> > Subject: [gmx-users] gmx distance > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > > Helecho "3 4"| g_distlo, i want to introduce a coomand in Gromacs 5.0.4 > with the initial echo "3 4"| g_dist. Should i use gmx distance echo "3 4"| > g_dist and the rest of the commnand? This is the complete command i want to > use echo "3 4"| g_dist -f dppc128_1-nj-ct-nobox.xtc -s dppc128_1.tpr -o > dppc128-Dpp.xvg -n Dpp.ndx -b 20000. Or how should i use that command on > gromacs 5.0.4? Because i read the g_dist in gromacs 5.0 has been modified. > Thanks > > ------------------------------ > > Message: 4 > Date: Mon, 8 Jun 2015 14:07:27 -0600 > From: Alex <[email protected]> > To: Discussion list for GROMACS users <[email protected]> > Subject: [gmx-users] cudaStreamSynchronize failed in cu_blockwait_nb > Message-ID: > <CAMJZ6qEE6DdbN7vf4N7WhdMh1=usB-WbFWY-acFfDhfg=- > [email protected]> > Content-Type: text/plain; charset=UTF-8 > > Hi all, > > I am running a GPU-accelerated test (GMX 5.0.5) and, after about 60K steps > of what seems to be a huge speed-up, I get the error from the subject with > the following comment: "unspecified launch failure." > > This is on an 8-core (16-thread) Intel CPU and two Tesla cards. The run > command is: > > mdrun -ntomp 4 <file directives> > > I saw some previous messages on this error, but not sure there's a > solution. > Any thoughts? I will provide any additional info as needed. If there are > additional options necessary to debug etc, could you provide the exact > command line? > > Thanks, > > Alex > > > ------------------------------ > > Message: 5 > Date: Mon, 8 Jun 2015 14:25:03 -0600 > From: Alex <[email protected]> > To: Discussion list for GROMACS users <[email protected]> > Subject: Re: [gmx-users] cudaStreamSynchronize failed in > cu_blockwait_nb > Message-ID: > <CAMJZ6qEs9_8-Jq8m6FovmZB6siiKR3UAZxY= > [email protected]> > Content-Type: text/plain; charset=UTF-8 > > Additional info: > > The base system is a SuperMicro X8DTG-D motherboard with dual Xeon E5620 > CPUs at 2.4 GHz, and 24 GB of DDR3 ECC RAM > > The GPUs are two NVidia Tesla C2075s > > Running under Ubuntu 14.04 LTS 64-bit, kernel 3.13.0-53, with CUDA 7.0, > installed via the NVIDIA-provided .deb file, > cuda-repo-ubuntu1404-7-0-local_7.0-28_amd64.deb, followed by the usual > apt-get update/upgrade. > > Nvcc reports version 7.0.27. > > GMX version is 5.0.5, locally built, with auto-detected options, including > "GMX_GPU ON", and "GMX_SIMD SSE4.1" > > On Mon, Jun 8, 2015 at 2:07 PM, Alex <[email protected]> wrote: > > > Hi all, > > > > I am running a GPU-accelerated test (GMX 5.0.5) and, after about 60K > steps > > of what seems to be a huge speed-up, I get the error from the subject > with > > the following comment: "unspecified launch failure." > > > > This is on an 8-core (16-thread) Intel CPU and two Tesla cards. The run > > command is: > > > > mdrun -ntomp 4 <file directives> > > > > I saw some previous messages on this error, but not sure there's a > > solution. > > Any thoughts? I will provide any additional info as needed. If there are > > additional options necessary to debug etc, could you provide the exact > > command line? > > > > Thanks, > > > > Alex > > > > > ------------------------------ > > Message: 6 > Date: Mon, 8 Jun 2015 21:18:08 +0000 (UTC) > From: Marawan Hussien <[email protected]> > To: "[email protected]" > <[email protected]> > Subject: [gmx-users] Immediate PhD Opening In Computational Structural > Biology Of Membrane Proteins > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=UTF-8 > > Immediate PhD Opening In Dr. Khaled Barakat?s Lab, Faculty OfPharmacy, > University Of Alberta. > > ? > > Specialization:?Computational Structural Biology Of MembraneProteins > > ? > > Term:?4 Years Fully Funded PhD Studentship > > ? > > A four years fully funded PhD studentship is available immediatelyin the > computational chemistry and drug discovery lab of Dr. Khaled Barakat atthe > Faculty of Pharmacy, University of Alberta, Canada.?Successfulapplicants > will employ state-of-the-art computational techniques and highperformance > computing facilities accessible to the lab to work on thestructural biology > of membrane proteins. > > > ? > Applicants should have good undergraduate record in a research > richenvironment. They should also have strong communication skills, and an > abilityto collaborate effectively. > > > ? > The following qualifications are essential: > > > ? > 1.????????????M.Sc. degree (or equivalenteg: first class honor) in > chemistry, physics, or a related discipline (completedor near completion) > as well as outstanding B.Sc. graduates (with a 3.5/4.0 orhigher GPA). > > 2.????????????Strong aptitudes and in depthpassion in physical chemistry > and in mathematics. > > 3.????????????Interest in biochemistry,physiology, computer simulations. > > 4.????????????Familiarity with UNIX/Linuxoperating systems and python > scripting. > > 5.????????????At least one first authorpublication in a closely related > field. > > 6.????????????Familiarity withcomputational structural > biology/bioinformatics techniques, such as homologymodeling, classical MD > simulation, docking, etc. > > 7.????????????Experience with at least oneof the software packages for > atomistic biological simulations, such as AMBER,NAMD, GROMACS is > recommended. > > > Initial appointment will be for four years; this can be increased up to 5 > yearsdepending on the availability of funding. > > > To apply for this position, please send your most updated CV and a > briefstatement of research interests, along with the names and contact > informationof at least two referees, to:?Dr. Khaled Barakat (email:? > [email protected]) > > > ? > > ? > > ? > > ? > > > ------------------------------ > > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > > End of gromacs.org_gmx-users Digest, Vol 134, Issue 45 > ****************************************************** > -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
