[gmx-users] Catenation and Visualization
Hello everyone I have completed two independent 100 ns simulations of two differnt proteins in water. One is monomer and the other is trimer. Both simulations were allowed to run for 50 ns intially, after visulation, trajectories were 'correct' and then extended the simulation to 100 ns. Now after completion and catenation, when i converted the .xtc into movie.pdb using trjconv, the molecule seems broken in all the frames and i am not able to view it in cartoon style. Moreover, when i load the .pdb file of monomer or trimer in Pymol, Always two files are getting uploaded. I dont know what is the other file but it remains 'static' when i play the movie. Is this visualization problem or i madd a mistake in catenation? Can someone plz give insight With Regards Sent from my iPhone -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS
On 4/21/16 4:30 PM, Pedro Lacerda wrote: Hi Mark, I starting converting from AMBER (according to the paper) to GROMACS and comparing the results. Please explain in more words what this constant of two mean or how can I handle it. Ignoring it and just converting the units, I got these results It's force field convention, just different notation. Sometimes different force fields or programs use Rmin/2, Rmin, or sigma. They're easily converted, e.g.: sigma = (Rmin/2)*2*2^(-1/6) and in GROMACS the units are nm so you need an additional multiplication by 0.1 to convert A -> nm. AMBER (table 2a) Rmin/2 (Å) epsilon (kcal/mol) Zn2+ 1.10E+00 1.25E-02 Mg2+ 7.93E-01 8.95E-01 Ca2+ 1.71E+00 4.60E-01 AMBER converted R (nm) epsilon (kJ/mol) Zn2+ 2.20E+01 5.23E-02 Mg2+ 1.59E+01 3.74E+00 Ca2+ 3.43E+01 1.92E+00 amber99sb-ildn.ff/ffnonbonded.itp sigma (nm) epsilon (kJ/mol) Zn2+ 1.96E-01 5.23E-02 Mg2+ 1.41E-01 3.74E+00 Ca2+ 3.40E-01 3.60E-01 I got exact matches for epsilon in Zn and Mg, but not for Ca. Also the difference on sigma was in the order Å/10, except for Zn which was relatively significant. See above for the proper way to convert Rmin/2 to sigma. As for Ca, probably the parameters are coming from a different source. I don't know what "Table 2a" means or what paper it's from, but you need to verify that the source of parameters is compatible or that you understand where differences are coming from. -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 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Installation Problem... No command 'gmx' found
Thanks everyone. For your quick reply and support. On Thu, Apr 21, 2016 at 10:37 PM, Justin Lemkulwrote: > > > On 4/21/16 9:35 AM, Sotirios Dionysios I. Papadatos wrote: > >> Hi, in my case gmx is only needed for certain commands. For example >> pdb2gmx is working if I use it solo, not with gmx. It's worth a shot. >> >> > This is true for versions in the 5.0.x series; they can be called via gmx > or through the old syntax without it because the commands are all installed > as links to gmx. In 5.1.x this will not work; gmx/gmx_mpi (depending on > the installation) is mandatory. > > -Justin > > > >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Email >> Gmail Pribadi >> Sent: Thursday, April 21, 2016 9:18 AM >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Installation Problem... No command 'gmx' found >> >> Hi, >> >> Try gmx [command] . Ex. gmx mdrun -option >> >> Regards, >> >> >> Husen >> >> On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote: >>> >>> Hi, >>> >>> Try gmx_mpi. >>> >>> Regards >>> Terry >>> >>> >>> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir < imrul.reza.shis...@gmail.com> wrote: Dear all user I install gromacs in my laptop its perfectly ok. But i have problem to install in my desktop there i face problem. In my desktop i want to compile with cuda accelerator and MPI option. I install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all this driver is ok. For gromacs i run this installation command. tar -xzvf gromacs-5.1.2.tar.gz cd gromacs-5.1.2.tar.gz mkdir build cd build CMAKE -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on make -j16 make check sudo make install -j16 source /usr/local/gromacs/bin/GMXRC In the installation procedure i dont find any error. All 26 test completed without error. But when i try to run "gmx or gmx help" There is error no command gmx found. I need your guidance. Best Regards -- *Md Imrul Reza Shishir* -- 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 gmx-users-requ...@gromacs.org. >>> -- >>> 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 gmx-users-requ...@gromacs.org. >>> >> -- >> 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 gmx-users-requ...@gromacs.org. >> >> > -- > == > > 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 > > jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org. > -- *Md Imrul Reza Shishir* Master Student *Inha University* *CRC for NanoCellulose Future Composites* 36 Getbeol-ro, Yeonsu-gu Incheon 21999 South Korea -- 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 gmx-users-requ...@gromacs.org.
[gmx-users] Volume of system
hi Gmx experts i want to calculate Volume corresponding to the one molar standard state. is there any tool in gromacs to do that. i read about gmx density. Background: i have Protein-ligand complex simulation and i need to find energy of restraints which requires Volume. Thanks in advance Sana Saeed Khan, Research Assistant Chemoinformatics Lab Graduate Student, MS bioinfo Department of Bioinformatics Soongsil University, Seoul, South Korea. -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU
Hi Stéphane, Did you see the following or similar output from running /path/to/cuda/samples/1_Utilities/deviceQuery/deviceQuery when GROMACS wasn't able to detect GPU? ./deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) cudaGetDeviceCount returned 35 -> CUDA driver version is insufficient for CUDA runtime version Result = FAIL In my case this happens. Thanks, Tim At 2016-04-22 05:39:08, "Téletchéa Stéphane"wrote: >Le 21/04/2016 03:54, treinz a écrit : >> Hi, >> >> >> Can you also explain why the function calls to cudaDriverGetVersion() and >> cudaRuntimeGetVersion() both return 0, as in >>CUDA driver:0.0 >>CUDA runtime: 0.0 >> Thanks, >> Tim > >Hi all, > >As I already posted on the list, it seems the combination of gromacs + >cuda is tedious, >I had not time to dig it further, but wrote down what worked for me: > >http://www.steletch.org/spip.php?article89 > >The driver version was very close from the drivers included in the >default ubuntu >installation, nvidia-smi was working fine also, but gromacs was not able >to detect it. > >Using the driver from the cuda toolkit solved the problem for me. >I only sent a mail on the mailing list, if I have time to dig further >I'll try to provide more >insight and a proper bug report. Up to now you can check if the driver >version is the one >expected from the cuda toolkit (nvidia-smi -a). > >HTH, > >Stéphane > >-- >Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein >Design In Silico >UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes >cedex 03, France >Tél : +33 251 125 636 / Fax : +33 251 125 632 >http://www.ufip.univ-nantes.fr/ -http://www.steletch.org > >-- >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 gmx-users-requ...@gromacs.org. -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS
Hi Mark, I starting converting from AMBER (according to the paper) to GROMACS and comparing the results. Please explain in more words what this constant of two mean or how can I handle it. Ignoring it and just converting the units, I got these results AMBER (table 2a) Rmin/2 (Å) epsilon (kcal/mol) Zn2+ 1.10E+00 1.25E-02 Mg2+ 7.93E-01 8.95E-01 Ca2+ 1.71E+00 4.60E-01 AMBER converted R (nm) epsilon (kJ/mol) Zn2+ 2.20E+01 5.23E-02 Mg2+ 1.59E+01 3.74E+00 Ca2+ 3.43E+01 1.92E+00 amber99sb-ildn.ff/ffnonbonded.itp sigma (nm) epsilon (kJ/mol) Zn2+ 1.96E-01 5.23E-02 Mg2+ 1.41E-01 3.74E+00 Ca2+ 3.40E-01 3.60E-01 I got exact matches for epsilon in Zn and Mg, but not for Ca. Also the difference on sigma was in the order Å/10, except for Zn which was relatively significant. (I'm expecting that Mailman render the table into plain text relatively well, so if this post go with bad formatting I'll post again) Very thanks Pedro 2016-04-18 21:29 GMT-03:00 Mark Abraham: > Hi, > > Convert the units and absorb the factor of two to the minus six. Compare > with other ions present in both representations of such force fields. > > Mark > > On Tue, 19 Apr 2016 02:21 Pedro Lacerda wrote: > > > Hi Gromacs users, > > > > We are planning a simulation with a metallic (fe+2) attached on the > > protein. The parameters found in [1] cannot be directly inserted on > > ffnonbonded.itp because equation 1 of [1] and equation 4.5 of [2] are > > slightly different. > > > > Theoreticaly these Lennard-Jones parameters could be used in any PME > based > > force field, but it was derived and tested using the AMBER software and > > potential, so it is our current force field of choice. In > > amber99sb-ildn/ffnonbonded.itp the long range interactions are described > in > > terms of epsilon (kJ/mol) and sigma (Rmin; nm). > > > > Eq 1: > > > > Lj = 4e ((R/r)^12 - (R/r)^6) > > > > Eq 4.5: > > > > Lj = e ((R/r)^12 - 2(R/r)^6) > > > > Seems that Rmin values are written as Rmin/2 in AMBER files avoiding some > > calculations to optimize the software. But this occurs at implementation > > level and probably does not have correspondence with the paper. > > > > My question is how can I adapt these parameters so they can be used in > > Gromacs? > > > > (Sorry about the previous email, now the title is correct) > > > > [1] > > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728907/pdf/nihms481931.pdf > > > > [2] ftp://ftp.gromacs.org/pub/manual/manual-5.1.2.pdf > > > > [3] http://comments.gmane.org/gmane.science.biology.gromacs.user/82242 > > > > > > Cheers, > > > > Pedro Lacerda > > -- > > 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 gmx-users-requ...@gromacs.org. > > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
[gmx-users] vdwradii issue
Dear Gmx-Users Currently i'm having this kind of sticky warning when i am doing gmx solvate or gmx editconf (ff was charmm and oplsa). However i copied vdwradii.dat in my working directory, or use -vdwread flag still get this warning..Please how to get rid off of this Warning! WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. NOTE: From version 5.0 gmx uses the Van der Waals radiifrom the source below. This means the results may be differentcompared to previous GROMACS versions. Please give a some help! Thanks. (Im using gromacs/5.1.1 version) Khatnaa -- 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 gmx-users-requ...@gromacs.org.
[gmx-users] vdwradii issue
Dear Gmx-Users Currently i'm having this kind of sticky warning when i am doing gmx solvate or gmx editconf (ff was charmm and oplsa). However i copied vdwradii.dat in my working directory, or use -vdwread flag still get this warning..Please how to get rid off of this Warning! WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. NOTE: From version 5.0 gmx uses the Van der Waals radiifrom the source below. This means the results may be differentcompared to previous GROMACS versions. Please give a some help! Thanks. (Im using gromacs/5.1.1 version) Khatnaa -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU
On Thu, Apr 21, 2016 at 3:54 AM, treinzwrote: > Hi, > > > Can you also explain why the function calls to cudaDriverGetVersion() and > cudaRuntimeGetVersion() both return 0, as in Not really, but it is the normal behavior on hosts where the runtime is not compatible with the driver or there is simply no driver installed. Cheers, -- Szilárd >>> CUDA driver:0.0 >>> CUDA runtime: 0.0 > > > Thanks, > Tim > At 2016-04-21 08:49:17, "Szilárd Páll" wrote: >>On Thu, Apr 21, 2016 at 12:22 AM, treinz wrote: >>> Hi all, >>> >>> >>> I recently built 5.1.2 with GPU support and the config options are: >>> >>> >>> module load cuda/7.5.18 >>> cmake .. -DCMAKE_C_COMPILER=gcc-4.9 \ >>> -DCMAKE_CXX_COMPILER=g++-4.9 \ >>> -DGMX_MPI=OFF \ >>> -DGMX_THREAD_MPI=ON \ >>> -DGMX_GPU=ON \ >>> -DCMAKE_PREFIX_PATH=$HOME/local \ >>> -DCMAKE_INSTALL_PREFIX=$HOME/local/gromacs/grid_frontend \ >>> -DGMX_BUILD_OWN_FFTW=ON \ >>> -DGMX_DEFAULT_SUFFIX=OFF \ >>> -DGMX_BINARY_SUFFIX=_gpu \ >>> -DGMX_LIBS_SUFFIX=_gpu >>> >>> >>> and the installation was successful. But when I tried running mdrun, it >>> wasn't able to detect the GPU: >>> >>> >>> Build OS/arch: Linux 2.6.32-573.1.1.el6.x86_64 x86_64 >>> Build CPU vendor: GenuineIntel >>> Build CPU brand:Intel(R) Xeon(R) CPU E5-2620 v3 @ 2.40GHz >>> Build CPU family: 6 Model: 63 Stepping: 2 >>> Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt >>> lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd >>> rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic >>> C compiler: /net/noble/vol1/home/dejunlin/local/bin/mpicc GNU 4.9.3 >>> C compiler flags:-march=core-avx2-Wextra >>> -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall >>> -Wno-unused -Wunused-value -Wunused-parameter -O3 -DNDEBUG >>> -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds >>> C++ compiler: /net/noble/vol1/home/dejunlin/local/bin/mpicxx GNU 4.9.3 >>> C++ compiler flags: -march=core-avx2-Wextra >>> -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function >>> -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds >>> Boost version: 1.59.0 (external) >>> CUDA compiler: >>> /net/gs/vol3/software/modules-sw/cuda/7.5.18/Linux/RHEL6/x86_64/bin/nvcc >>> nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2015 NVIDIA >>> Corporation;Built on Tue_Aug_11_14:27:32_CDT_2015;Cuda compilation tools, >>> release 7.5, V7.5.17 >>> CUDA compiler >>> flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_52,code=compute_52;-use_fast_math;; >>> >>> ;-march=core-avx2;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds; >>> CUDA driver:0.0 >>> CUDA runtime: 0.0 >>> >>> >>> NOTE: Error occurred during GPU detection: >>> CUDA driver version is insufficient for CUDA runtime version >>> Can not use GPU acceleration, will fall back to CPU kernels. >>> >> >>^^^ This is the message you should be focusing on. For some reason, >>the runtime mdrun was compiled with is incompatible with the driver. >>This should not be the case if the driver is indeed 352.xx (which is >>driver API v 7.5) as shown below and the runtime API v 7.5. >> >>> The command lines for this run is: >>> >>> >>> module load cuda/7.5.18 >>> source $HOME/local/gromacs/grid_frontend/bin/GMXRC >>> env >>> nvidia-smi -a >>> gmx_gpu mdrun -ntmpi 24 -ntomp 1 -gpu_id 1 -deffnm >> >>FYI: That's going to be inefficient, probably the worst possible >>option in fact. Try 1-6 ranks/GPU. >> >>> >>> I look at the stdout from nvidia-smi, it looks like the nvidia driver was >>> installed (there are 4 GPUs but I'm only showing one of them): >>> >>> >>> ==NVSMI LOG== >>> >>> >>> Timestamp : Wed Apr 20 15:05:52 2016 >>> Driver Version : 352.39 >>> >>> >>> Attached GPUs : 4 >>> GPU :02:00.0 >>> Product Name: Tesla K40c >>> Product Brand : Tesla >>> Display Mode: Disabled >>> Display Active : Disabled >>> Persistence Mode: Disabled >>> Accounting Mode : Disabled >>> Accounting Mode Buffer Size : 1920 >>> Driver Model >>> Current : N/A >>> Pending : N/A >>> Serial Number : 0321715040048 >>> GPU UUID: >>>
Re: [gmx-users] Moving this mailing list to Discourse format
Hi Mark, many thanks. At the end it is really just a question if the user has flexibility over how to visualise the communications. I'm happy to hear that the old-fashioned email way would still have (some) support :-) I hope you get sufficient feedback and support from the community. Cheers, Hannes. On Thu, 21 Apr 2016 08:47:56 + Mark Abrahamwrote: > Hi Hannes, > > Yes, previous discussion has identified this as a likely key feature, > and thanks for adding confirmation of that. Discourse can be > integrated with functionality for replying to threads from email to > suit people who want that kind of small change to their workflows; > that will indeed suit simple discussions. Obviously there's > configurable email activity digests and notifications also, which > provide links to the forum proper. > > Mark > > On Thu, Apr 21, 2016 at 9:52 AM Hannes Loeffler > wrote: > > > On Thu, 21 Apr 2016 07:11:42 + > > Mark Abraham wrote: > > > > > Hi people, > > > > > > As part of the new BioExcel project (http://bioexcel.eu/) that > > > supports biomolecular research with codes including GROMACS, we're > > > exploring migrating the gmx-users mailing list to the Discourse > > > format. You can see an example at http://try.discourse.org! This > > > has a number of immediate advantages, including attachments, > > > single-click sign-up, tagging, voting and contributing to old > > > discussions. We might also integrate features like replying to > > > threads via email, or real-time chat. We also know such a change > > > might be something people don't like, and we would like to get a > > > feel for that. The community should like its forum, after > > > all! :-) So please let us know how you feel at > > > http://goo.gl/forms/k8lhTliffO. > > > > I think such a discussion would need a bit more space than just a > > few pre-canned questions. > > > > I am on various mailing lists and happy with my email client as a > > central "collector" of all those discussions. I am personally not > > fond of another web page interface with its very own features, > > bells and whistles and what not, but typically unlike any other > > existing one. And this is in essence the major shortcoming unless > > it would be still possible to receive all messages through a > > mailing list as it is now. > > > > Cheers, > > Hannes. > > -- > > 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 gmx-users-requ...@gromacs.org. > > -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Installation Problem... No command 'gmx' found
On 4/21/16 9:35 AM, Sotirios Dionysios I. Papadatos wrote: Hi, in my case gmx is only needed for certain commands. For example pdb2gmx is working if I use it solo, not with gmx. It's worth a shot. This is true for versions in the 5.0.x series; they can be called via gmx or through the old syntax without it because the commands are all installed as links to gmx. In 5.1.x this will not work; gmx/gmx_mpi (depending on the installation) is mandatory. -Justin From: gromacs.org_gmx-users-boun...@maillist.sys.kth.seon behalf of Email Gmail Pribadi Sent: Thursday, April 21, 2016 9:18 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Installation Problem... No command 'gmx' found Hi, Try gmx [command] . Ex. gmx mdrun -option Regards, Husen On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote: Hi, Try gmx_mpi. Regards Terry On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir wrote: Dear all user I install gromacs in my laptop its perfectly ok. But i have problem to install in my desktop there i face problem. In my desktop i want to compile with cuda accelerator and MPI option. I install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all this driver is ok. For gromacs i run this installation command. tar -xzvf gromacs-5.1.2.tar.gz cd gromacs-5.1.2.tar.gz mkdir build cd build CMAKE -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on make -j16 make check sudo make install -j16 source /usr/local/gromacs/bin/GMXRC In the installation procedure i dont find any error. All 26 test completed without error. But when i try to run "gmx or gmx help" There is error no command gmx found. I need your guidance. Best Regards -- *Md Imrul Reza Shishir* -- 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 gmx-users-requ...@gromacs.org. -- 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 gmx-users-requ...@gromacs.org. -- 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 gmx-users-requ...@gromacs.org. -- == 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 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Installation Problem... No command 'gmx' found
Hi, in my case gmx is only needed for certain commands. For example pdb2gmx is working if I use it solo, not with gmx. It's worth a shot. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.seon behalf of Email Gmail Pribadi Sent: Thursday, April 21, 2016 9:18 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Installation Problem... No command 'gmx' found Hi, Try gmx [command] . Ex. gmx mdrun -option Regards, Husen > On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote: > > Hi, > > Try gmx_mpi. > > Regards > Terry > > >> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir >> wrote: >> >> Dear all user >> >> I install gromacs in my laptop its perfectly ok. But i have problem to >> install in my desktop there i face problem. >> In my desktop i want to compile with cuda accelerator and MPI option. I >> install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all >> this driver is ok. >> >> For gromacs i run this installation command. >> >> tar -xzvf gromacs-5.1.2.tar.gz >> cd gromacs-5.1.2.tar.gz >> mkdir build >> cd build >> CMAKE -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on >> -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on >> make -j16 >> make check >> sudo make install -j16 >> >> source /usr/local/gromacs/bin/GMXRC >> >> In the installation procedure i dont find any error. All 26 test completed >> without error. >> >> But when i try to run "gmx or gmx help" >> >> There is error no command gmx found. I need your guidance. >> >> Best Regards >> >> -- >> *Md Imrul Reza Shishir* >> -- >> 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 gmx-users-requ...@gromacs.org. > -- > 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 gmx-users-requ...@gromacs.org. -- 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 gmx-users-requ...@gromacs.org. -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] sugar puckering
Le 21/04/2016 04:24, bharat gupta a écrit : Dear Gmx Users, I am interested in calculating cremer-pople parameters for a trisachharide ligand from its simulation docked with a protein. I found one tool g_puckering for calculating the parameters but it was written for Gromacs version 4.0.x and I am using version 5.0.4. I am not able to compile this tool for my current version of gromacs. So can anybody tell me how can I calculate such parameters in gromacs ?? 1 - contact the authors 2 - adjust the code (I'm interested if you do it ...) 3 - compile it using the version it was meant for, if it parses xtc files it should not matter a lot ... Best, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] empty index group
On 4/21/16 7:29 AM, David Newman wrote: Hi, So on Gromacs 4.6.5, I'm using the make_ndx command to try to create a custom index of a binding pocket on my protein of interest, I want to group 5 non-contiguous residues, I can index them separately and tried to group them with & but that creates an empty group error because I guess it is for linking separate options together not separate instances of the same option. Is there a way to achieve what I'm after? Your problem is that you used &. Atoms cannot be in one residue and simultaneously in another. You need the "or" operator, |, e.g.: r 10 | r 20 | r 30 | r 40 | r 50 because atoms can be in residue 10 OR residue 20 OR ... -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 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org.
[gmx-users] empty index group
Hi, So on Gromacs 4.6.5, I'm using the make_ndx command to try to create a custom index of a binding pocket on my protein of interest, I want to group 5 non-contiguous residues, I can index them separately and tried to group them with & but that creates an empty group error because I guess it is for linking separate options together not separate instances of the same option. Is there a way to achieve what I'm after? Thanks, David -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem regarding cut-off and the PME grid spacing
On 4/21/16 6:57 AM, Tuhin Samanta wrote: please check it... [ moleculetype ] ; molname nrexcl HOD 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_116 1HOD OW 1 -0.8476 2 opls_117 1HOD HW 1 0.4238 3 opls_805 1HOD DW 1 0.4238 #ifndef FLEXIBLE ; [ settles ] ; OWfunct doh dhh ; 10.101 0.16500 ;[ exclusions ] ;1 2 3 ;2 1 3 ;3 1 2 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 0.1 345000 1 3 1 0.102 266292 0.102 266292 [ angles ] ; i j k funct angle force.c. 2 1 3 1 105.7 583 105.7 583 Of course this crashes - you're trying to use a 2-fs time step without any constraints. Reduce dt or treat the water model as rigid. -Justin Thanks, Tuhin On Thu, Apr 21, 2016 at 3:20 PM, Justin Lemkulwrote: On 4/21/16 3:32 AM, Tuhin Samanta wrote: The topology file for my system - HOD System like that --- #include "oplsaa.ff/forcefield.itp" ; Include hod topology #include "hod.itp" [ system ] ;Name HOD [ molecules ] ; Compound#mols HOD102 .mdp file is like that - (FOR Energy minimization) ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 0.1 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 20; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) constraints = none For Equilibritaion (NVT) title = NVT equilibration of W10 RM cpp = /lib/cpp include = -I../top integrator = md; leap-frog integrator nsteps = 50 ; 2 * 1 = 20 ns dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.1 ns nstvout = 100 ; save velocities every 0.1 ns nstenergy = 100 ; save energies every 0.1 ns nstlog = 100 ; update log file every 0.1 ns ; Bond parameters continuation= yes ; continuation from previous run constraint_algorithm = lincs; holonomic constraints constraints = none ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT optimize_fft= yes ; Temperature coupling is on tcoupl = Berendsen ; modified Berendsen thermostat tc-grps = System; two coupling groups - more accurate tau_t = 1.0 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution Please take a look . I am getting the error like that -- 4 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. If you want I can send you my .itp file also. Yes, that's actually rather important; the .top itself just #includes
Re: [gmx-users] problem regarding cut-off and the PME grid spacing
please check it... [ moleculetype ] ; molname nrexcl HOD 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_116 1HOD OW 1 -0.8476 2 opls_117 1HOD HW 1 0.4238 3 opls_805 1HOD DW 1 0.4238 #ifndef FLEXIBLE ; [ settles ] ; OWfunct doh dhh ; 10.101 0.16500 ;[ exclusions ] ;1 2 3 ;2 1 3 ;3 1 2 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 0.1 345000 1 3 1 0.102 266292 0.102 266292 [ angles ] ; i j k funct angle force.c. 2 1 3 1 105.7 583 105.7 583 Thanks, Tuhin On Thu, Apr 21, 2016 at 3:20 PM, Justin Lemkulwrote: > > > On 4/21/16 3:32 AM, Tuhin Samanta wrote: > >> The topology file for my system - HOD System like that --- >> >> >> >> #include "oplsaa.ff/forcefield.itp" >> >> ; Include hod topology >> #include "hod.itp" >> >> [ system ] >> ;Name >> HOD >> >> [ molecules ] >> ; Compound#mols >> HOD102 >> >> .mdp file is like that - >> >> (FOR Energy minimization) >> >> ; minim.mdp - used as input into grompp to generate em.tpr >> ; Parameters describing what to do, when to stop and what to save >> integrator = steep ; Algorithm (steep = steepest descent >> minimization) >> emtol = 0.1 ; Stop minimization when the maximum force >> < 1000.0 kJ/mol/nm >> emstep = 0.01 ; Energy step size >> nsteps = 20; Maximum number of (minimization) steps >> to >> perform >> >> ; Parameters describing how to find the neighbors of each atom and how to >> calculate the interactions >> nstlist = 1 ; Frequency to update the neighbor list >> and >> long range forces >> ns_type = grid ; Method to determine neighbor list >> (simple, grid) >> rlist = 1.0 ; Cut-off for making neighbor list (short >> range forces) >> coulombtype = PME ; Treatment of long range electrostatic >> interactions >> rcoulomb= 1.0 ; Short-range electrostatic cut-off >> rvdw= 1.0 ; Short-range Van der Waals cut-off >> pbc = xyz ; Periodic Boundary Conditions (yes/no) >> constraints = none >> >> For Equilibritaion (NVT) >> >> title = NVT equilibration of W10 RM >> cpp = /lib/cpp >> include = -I../top >> integrator = md; leap-frog integrator >> nsteps = 50 ; 2 * 1 = 20 ns >> dt = 0.002 ; 2 fs >> ; Output control >> nstxout = 100 ; save coordinates every 0.1 ns >> nstvout = 100 ; save velocities every 0.1 ns >> nstenergy = 100 ; save energies every 0.1 ns >> nstlog = 100 ; update log file every 0.1 ns >> ; Bond parameters >> continuation= yes ; continuation from previous run >> constraint_algorithm = lincs; holonomic constraints >> constraints = none ; all bonds (even heavy atom-H bonds) >> constrained >> lincs_iter = 1 ; accuracy of LINCS >> lincs_order = 4 ; also related to accuracy >> ; Neighborsearching >> ns_type = grid ; search neighboring grid cells >> nstlist = 10 ; 10 fs >> rlist = 1.0 ; short-range neighborlist cutoff (in nm) >> rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) >> rvdw= 1.0 ; short-range van der Waals cutoff (in nm) >> ; Electrostatics >> coulombtype = PME ; Particle Mesh Ewald for long-range >> electrostatics >> pme_order = 4 ; cubic interpolation >> fourierspacing = 0.16 ; grid spacing for FFT >> optimize_fft= yes >> ; Temperature coupling is on >> tcoupl = Berendsen ; modified Berendsen thermostat >> tc-grps = System; two coupling groups - more accurate >> tau_t = 1.0 ; time constant, in ps >> ref_t = 300 ; reference temperature, one for each >> group >> ; Pressure coupling is off >> pcoupl = no; no pressure coupling in NVT >> ; Periodic boundary conditions >> pbc = xyz ; 3-D PBC >> ; Dispersion correction >> DispCorr= EnerPres ; account for cut-off vdW scheme >> ; Velocity generation >> gen_vel = yes ; assign velocities from Maxwell >> distribution >> >> >> Please take a look . I am getting the error like that -- 4 particles >> communicated to PME node 4 are more than 2/3 times the cut-off out of the >> domain decomposition cell of their charge group in dimension x. This >> usually means that your system is not well equilibrated. >> >> If you want I can
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 119
Hi, Indeed, Link atoms have to be added to the .gro file. The atom indexing in the .gro file is not used, so no need to renumber. A simple editconf can do that for you if too, if you would like to have the numbering correct. However, you need to adjust the total number of atoms at the top of the .gro file. for the bonded interactions, you should remove the gb_x , because these defines contain the bond type information as well. Easiest is to add a ';' like this 1851 1853 2 ; gb_10 which means that what comes after is ignored. good luck, Gerrit Message: 3 Date: Thu, 21 Apr 2016 17:43:47 +0900 From: bharat guptaTo: Discussion list for GROMACS users Subject: Re: [gmx-users] Defining LA atoms in .gro file Message-ID: Content-Type: text/plain; charset=UTF-8 Dear GMX Users, I am trying to perform QM/MM simulation for my system and I need to define LA for the boundary between QM and MM region. I have the boundary regions but I don't know how to add them in the gro file. Do I have to manually modify the .gro file, if that's the case, adding, them manually how do I renumber the rest of the atoms and residues? Here's what I have done: 3715YWR H21 3562 4.283 4.647 4.755 -1.1354 1.0843 -0.8713 372XXX LA 3563 2.475 3.856 2.040 -0.0020 -0.1066 0.1995 373XXX LA 3564 0.475 3.856 2.040 -0.0020 -0.1066 0.1995 374XXX LA 3565 1.475 3.856 2.040 -0.0020 -0.1066 0.1995 375XXX LA 3566 3.475 3.856 2.040 -0.0020 -0.1066 0.1995 376XXX LA 3567 0.875 3.856 2.040 -0.0020 -0.1066 0.1995 377XXX LA 3568 1.575 3.856 2.040 -0.0020 -0.1066 0.1995 372SOL OW 3563 3.414 3.445 2.243 -0.1786 -0.5561 0.4692 372SOLHW1 3564 3.479 3.440 2.167 0.5613 -1.1084 1.1215 372SOLHW2 3565 3.329 3.488 2.212 0.4389 0.0440 -0.4374 373SOL OW 3566 1.589 3.334 2.348 0.6300 0.1793 -0.1279 373SOLHW1 3567 1.639 3.413 2.384 1.2205 0.0166 -0.5746 373SOLHW2 3568 1.588 3.337 2.248 -1.5585 0.9770 -0.1508 374SOL OW 3569 5.280 6.227 4.070 0.5862 -0.1571 -0.6930 So, I added the LA atoms between atom no H21/3562 and OW/3563 manually. Please let me whether this is the correct way of adding the LA atoms ? Also, I need to modify the bond_types as well in the topology file to 5. Is this the correct way: 1851 1853 2gb_10 1853 1854 5gb_2 1853 1855 5gb_21 1855 1856 5gb_27 1855 1862 5gb_27 1856 1857 5gb_27 1857 1858 5gb_27 1858 1859 5gb_5 1858 1860 5gb_13 1860 1861 5gb_1 1862 1863 5gb_5 1862 1864 2gb_10 1864 1865 2gb_2 I haven't changed the values for C0 for the QM atoms but I have changed their type to 5. -- *Best Regards* BM -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] trouble with ca2+ atom and SEP recognition in Gromacs 5.1.1
On 4/20/16 3:56 PM, Jayant James wrote: Hi! All I have been running into some trouble with CA2+ recognition in GMX 5.1.1. So some back ground..I have a protein that I am trying to simulate that has three chains.First chain is 161 amino acids long, second one is about 200AA and the third one is about 280 AA long. They have their terminal residues given with OXT and "ter" is given after each chain. Also this protein has two phosphorylated serines that are input as SEP. Since I am having two SEP molecules I am using the option# 10 GROMOS96 43a1 force field, extended to include phosphorylated residues Below is the description of the calcium atoms in the input PDB file --- ATOM 1283 CA CA2+D 162 10.494 65.413 -1.733 1.00 78.08 C ATOM 1284 CA CA2+D 163 14.370 25.685 8.168 1.00 78.08 C ATOM 1285 CA CA2+D 164 18.826 35.294 3.395 1.00 78.08 C INPUT COMMAND -- gmx pdb2gmx -f start.pdb -p new -o new -merge all -ignh Concerns - 1) I am hit with error messages that tell me the calcium ions are not recognized (colored red). I'd appreciate a way to solve this. They're recognized just fine, but apparently they're disrupting a protein chain. A continuous chain has to be continuous with respect to residue type, otherwise pdb2gmx warns you that something is amiss. 2) Also the third chain having the SEP amino acids is not being recognizing!!! Colored blue You need to add SEP as a Protein entry in residuetypes.dat. 3) The third chain is 192 aa long. But the program tells that it recognizes only till 22 aa although a few lines this it seems like it recognizes till the 192nd aa See point #2. -Justin I'd appreciate any suggetions that would help me tide over these errors Thank you James *ERROR MESSAGE* -- Opening force field file /share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/aminoacids.r2b Reading start.pdb... Read 3572 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. Merged chains into joint molecule definitions at 2 places. There are 1 chains and 0 blocks of water and 443 residues with 3572 atoms chain #res #atoms 1 'D' 443 3572 All occupancies are one Opening force field file /share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/atomtypes.atp Atomtype 48 Reading residue database... (gromos43a1p) Opening force field file /share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Residue 101 Sorting it all out... Opening force field file /share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/aminoacids.hdb Opening force field file /share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/aminoacids.n.tdb Opening force field file /share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/aminoacids.c.tdb Back Off! I just backed up new.top to ./#new.top.2# Processing chain 1 'D' (3572 atoms, 443 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 679 donors and 705 acceptors were found. There are 937 hydrogen bonds Will use HISE for residue 223 Will use HISE for residue 35 Will use HISE for residue 102 Will use HISE for residue 173 Identified residue MET1 as a starting terminus. Warning: Residue CA2+162 in chain has different type (Other) from starting residue MET1 (Protein). Warning: Residue CA2+163 in chain has different type (Other) from starting residue MET1 (Protein). Warning: Residue CA2+164 in chain has different type (Other) from starting residue MET1 (Protein). Identified residue GLU161 as a ending terminus. Identified residue GLN202 as a starting terminus. Identified residue LYS288 as a ending terminus. Identified residue MET1 as a starting terminus. Warning: Residue SEP23 in chain has different type (Other) from starting residue MET1 (Protein). Warning: Residue SEP24 in chain has different type (Other) from starting residue MET1 (Protein). Warning: Residue ALA25 in chain has different type (Protein) from starting residue MET1 (Protein). Warning: Residue ASN26 in chain has different type (Protein) from starting residue MET1 (Protein). Warning: Residue TYR27 in chain has different type (Protein) from starting residue MET1 (Protein). Special Atom Distance matrix: MET1 MET45 MET47 MET60 MET80 MET81 MET85 SD7 SD349 SD368 SD470 SD625 SD633 SD665 MET45 SD349 2.333 MET47 SD368 3.175 1.004 MET60 SD470 1.883 0.496 1.457 MET80 SD625 1.769 0.820 1.424 0.683 MET81 SD633 2.065 0.981 1.341 1.050
Re: [gmx-users] Number of urea molecules for 2.1 M solution
On 4/21/16 3:00 AM, Divya Dube wrote: Dear all, How to calculate number of urea molecules required for a box size of 294.68 nm^3 for 2.1 M urea solution You have a volume, you have a desired concentration, C = n/V. -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 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem regarding cut-off and the PME grid spacing
On 4/21/16 3:32 AM, Tuhin Samanta wrote: The topology file for my system - HOD System like that --- #include "oplsaa.ff/forcefield.itp" ; Include hod topology #include "hod.itp" [ system ] ;Name HOD [ molecules ] ; Compound#mols HOD102 .mdp file is like that - (FOR Energy minimization) ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 0.1 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 20; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) constraints = none For Equilibritaion (NVT) title = NVT equilibration of W10 RM cpp = /lib/cpp include = -I../top integrator = md; leap-frog integrator nsteps = 50 ; 2 * 1 = 20 ns dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.1 ns nstvout = 100 ; save velocities every 0.1 ns nstenergy = 100 ; save energies every 0.1 ns nstlog = 100 ; update log file every 0.1 ns ; Bond parameters continuation= yes ; continuation from previous run constraint_algorithm = lincs; holonomic constraints constraints = none ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT optimize_fft= yes ; Temperature coupling is on tcoupl = Berendsen ; modified Berendsen thermostat tc-grps = System; two coupling groups - more accurate tau_t = 1.0 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution Please take a look . I am getting the error like that -- 4 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. If you want I can send you my .itp file also. Yes, that's actually rather important; the .top itself just #includes the .itp and therefore contains no useful information. -Justin Tuhin On Wed, Apr 20, 2016 at 10:52 PM, Justin Lemkulwrote: On 4/20/16 1:20 PM, Tuhin Samanta wrote: I have done the energy minimization many times by taking previously minimized structure. A box of water should be basically impossible to break. Either your .mdp or topology has problems. Since you've provided neither, there's not much anyone can do to help you. The diagnostic walkthrough that Mark linked is the best source of figuring it out. Short of that, provide us with your input topology and .mdp (copied and pasted if small enough for an email, or linked to a file-sharing service otherwise). -Justin On Wed, Apr 20, 2016 at 10:39 PM, Mark Abraham wrote: Hi, On Wed, 20 Apr 2016 19:04 Tuhin Samanta wrote: Thank Mark for your suggestion. I was trying to resolve the problem " 4 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the
Re: [gmx-users] NA or SOD in CHARMM36
On 4/21/16 4:56 AM, Jason Loo Siau Ee wrote: Hi all, I'm trying to simulate a protein-ligand complex in POPC membrane using the CHARMM36 forcefield, which I got from the Mackerell site and included in /share/gromacs/top/. Now when I run grompp I get the error "Fatal error: No such moleculetype SOD" despite the fact that I have #include "charmm36.ff/ions.itp" in my topology. A quick check on the ions.itp in charmm36.ff/ shows the following: [ moleculetype ] ; molname nrexcl NA 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 SOD 1 NA NA 1 1 Now as I understand sodium is called SOD in CHARMM, so shouldn't all the NA be SOD instead? As this is from the Mackerell site I'm going to assume there isn't an error here, so am I about the do something silly? Is there a reason for this discrepancy (like because genion only adds NA and not SOD)? I've noticed similar issues with other ions and the water models (SOL instead of TI3P). I'm guessing I should create a local copy of the modified itp files then? You should use NA; this is done to follow the GROMACS genion convention that ions are added by their all-caps elemental symbol. So your -pname in genion should be NA, which means NA is written to the topology file. SOD is just the atom type, which is only used by grompp when parsing the actual parameters. You shouldn't need to make any changes to the files. -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 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org.
[gmx-users] NA or SOD in CHARMM36
Hi all, I'm trying to simulate a protein-ligand complex in POPC membrane using the CHARMM36 forcefield, which I got from the Mackerell site and included in /share/gromacs/top/. Now when I run grompp I get the error "Fatal error: No such moleculetype SOD" despite the fact that I have #include "charmm36.ff/ions.itp" in my topology. A quick check on the ions.itp in charmm36.ff/ shows the following: [ moleculetype ] ; molname nrexcl NA 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 SOD 1 NA NA 1 1 Now as I understand sodium is called SOD in CHARMM, so shouldn't all the NA be SOD instead? As this is from the Mackerell site I'm going to assume there isn't an error here, so am I about the do something silly? Is there a reason for this discrepancy (like because genion only adds NA and not SOD)? I've noticed similar issues with other ions and the water models (SOL instead of TI3P). I'm guessing I should create a local copy of the modified itp files then? Regards, Jason Loo Confidentiality Disclaimer: This e-mail and any attachments are confidential and intended solely for the intended addressee and may also be privileged or exempt from disclosure under applicable law. If you are not the intended addressee, or have received this e-mail in error, please notify the sender immediately, delete it from your system and do not copy, disclose, distribute or otherwise act in reliance upon any part of this e-mail or its attachments. Taylor's Education Group does not accept responsibility for any loss arising from unauthorized access to, or interference with, any internet communications by any third party in reliance to this email, or from the transmission of any viruses. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of Taylor's Education Group. Replies to this e-mail may be monitored by Taylor's Education Group for operational or business reasons. -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Moving this mailing list to Discourse format
Hi Hannes, Yes, previous discussion has identified this as a likely key feature, and thanks for adding confirmation of that. Discourse can be integrated with functionality for replying to threads from email to suit people who want that kind of small change to their workflows; that will indeed suit simple discussions. Obviously there's configurable email activity digests and notifications also, which provide links to the forum proper. Mark On Thu, Apr 21, 2016 at 9:52 AM Hannes Loefflerwrote: > On Thu, 21 Apr 2016 07:11:42 + > Mark Abraham wrote: > > > Hi people, > > > > As part of the new BioExcel project (http://bioexcel.eu/) that > > supports biomolecular research with codes including GROMACS, we're > > exploring migrating the gmx-users mailing list to the Discourse > > format. You can see an example at http://try.discourse.org! This has > > a number of immediate advantages, including attachments, single-click > > sign-up, tagging, voting and contributing to old discussions. We > > might also integrate features like replying to threads via email, or > > real-time chat. We also know such a change might be something people > > don't like, and we would like to get a feel for that. The community > > should like its forum, after all! :-) So please let us know how you > > feel at http://goo.gl/forms/k8lhTliffO. > > I think such a discussion would need a bit more space than just a few > pre-canned questions. > > I am on various mailing lists and happy with my email client as a > central "collector" of all those discussions. I am personally not fond > of another web page interface with its very own features, bells and > whistles and what not, but typically unlike any other existing one. > And this is in essence the major shortcoming unless it would be still > possible to receive all messages through a mailing list as it is now. > > Cheers, > Hannes. > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Defining LA atoms in .gro file
Dear GMX Users, I am trying to perform QM/MM simulation for my system and I need to define LA for the boundary between QM and MM region. I have the boundary regions but I don't know how to add them in the gro file. Do I have to manually modify the .gro file, if that's the case, adding, them manually how do I renumber the rest of the atoms and residues? Here's what I have done: 3715YWR H21 3562 4.283 4.647 4.755 -1.1354 1.0843 -0.8713 372XXX LA 3563 2.475 3.856 2.040 -0.0020 -0.1066 0.1995 373XXX LA 3564 0.475 3.856 2.040 -0.0020 -0.1066 0.1995 374XXX LA 3565 1.475 3.856 2.040 -0.0020 -0.1066 0.1995 375XXX LA 3566 3.475 3.856 2.040 -0.0020 -0.1066 0.1995 376XXX LA 3567 0.875 3.856 2.040 -0.0020 -0.1066 0.1995 377XXX LA 3568 1.575 3.856 2.040 -0.0020 -0.1066 0.1995 372SOL OW 3563 3.414 3.445 2.243 -0.1786 -0.5561 0.4692 372SOLHW1 3564 3.479 3.440 2.167 0.5613 -1.1084 1.1215 372SOLHW2 3565 3.329 3.488 2.212 0.4389 0.0440 -0.4374 373SOL OW 3566 1.589 3.334 2.348 0.6300 0.1793 -0.1279 373SOLHW1 3567 1.639 3.413 2.384 1.2205 0.0166 -0.5746 373SOLHW2 3568 1.588 3.337 2.248 -1.5585 0.9770 -0.1508 374SOL OW 3569 5.280 6.227 4.070 0.5862 -0.1571 -0.6930 So, I added the LA atoms between atom no H21/3562 and OW/3563 manually. Please let me whether this is the correct way of adding the LA atoms ? Also, I need to modify the bond_types as well in the topology file to 5. Is this the correct way: 1851 1853 2gb_10 1853 1854 5gb_2 1853 1855 5gb_21 1855 1856 5gb_27 1855 1862 5gb_27 1856 1857 5gb_27 1857 1858 5gb_27 1858 1859 5gb_5 1858 1860 5gb_13 1860 1861 5gb_1 1862 1863 5gb_5 1862 1864 2gb_10 1864 1865 2gb_2 I haven't changed the values for C0 for the QM atoms but I have changed their type to 5. -- *Best Regards* BM -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Moving this mailing list to Discourse format
On Thu, 21 Apr 2016 07:11:42 + Mark Abrahamwrote: > Hi people, > > As part of the new BioExcel project (http://bioexcel.eu/) that > supports biomolecular research with codes including GROMACS, we're > exploring migrating the gmx-users mailing list to the Discourse > format. You can see an example at http://try.discourse.org! This has > a number of immediate advantages, including attachments, single-click > sign-up, tagging, voting and contributing to old discussions. We > might also integrate features like replying to threads via email, or > real-time chat. We also know such a change might be something people > don't like, and we would like to get a feel for that. The community > should like its forum, after all! :-) So please let us know how you > feel at http://goo.gl/forms/k8lhTliffO. I think such a discussion would need a bit more space than just a few pre-canned questions. I am on various mailing lists and happy with my email client as a central "collector" of all those discussions. I am personally not fond of another web page interface with its very own features, bells and whistles and what not, but typically unlike any other existing one. And this is in essence the major shortcoming unless it would be still possible to receive all messages through a mailing list as it is now. Cheers, Hannes. -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem regarding cut-off and the PME grid spacing
The topology file for my system - HOD System like that --- #include "oplsaa.ff/forcefield.itp" ; Include hod topology #include "hod.itp" [ system ] ;Name HOD [ molecules ] ; Compound#mols HOD102 .mdp file is like that - (FOR Energy minimization) ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 0.1 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 20; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) constraints = none For Equilibritaion (NVT) title = NVT equilibration of W10 RM cpp = /lib/cpp include = -I../top integrator = md; leap-frog integrator nsteps = 50 ; 2 * 1 = 20 ns dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.1 ns nstvout = 100 ; save velocities every 0.1 ns nstenergy = 100 ; save energies every 0.1 ns nstlog = 100 ; update log file every 0.1 ns ; Bond parameters continuation= yes ; continuation from previous run constraint_algorithm = lincs; holonomic constraints constraints = none ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT optimize_fft= yes ; Temperature coupling is on tcoupl = Berendsen ; modified Berendsen thermostat tc-grps = System; two coupling groups - more accurate tau_t = 1.0 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution Please take a look . I am getting the error like that -- 4 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. If you want I can send you my .itp file also. Tuhin On Wed, Apr 20, 2016 at 10:52 PM, Justin Lemkulwrote: > > > On 4/20/16 1:20 PM, Tuhin Samanta wrote: > >> I have done the energy minimization many times by taking previously >> minimized structure. >> >> > A box of water should be basically impossible to break. Either your .mdp > or topology has problems. Since you've provided neither, there's not much > anyone can do to help you. The diagnostic walkthrough that Mark linked is > the best source of figuring it out. Short of that, provide us with your > input topology and .mdp (copied and pasted if small enough for an email, or > linked to a file-sharing service otherwise). > > -Justin > > > >> >> On Wed, Apr 20, 2016 at 10:39 PM, Mark Abraham >> wrote: >> >> Hi, >>> >>> On Wed, 20 Apr 2016 19:04 Tuhin Samanta >>> wrote: >>> >>> Thank Mark for your suggestion. I was trying to resolve the problem " 4 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system
[gmx-users] Moving this mailing list to Discourse format
Hi people, As part of the new BioExcel project (http://bioexcel.eu/) that supports biomolecular research with codes including GROMACS, we're exploring migrating the gmx-users mailing list to the Discourse format. You can see an example at http://try.discourse.org! This has a number of immediate advantages, including attachments, single-click sign-up, tagging, voting and contributing to old discussions. We might also integrate features like replying to threads via email, or real-time chat. We also know such a change might be something people don't like, and we would like to get a feel for that. The community should like its forum, after all! :-) So please let us know how you feel at http://goo.gl/forms/k8lhTliffO. Cheers, Mark GROMACS development manager -- 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 gmx-users-requ...@gromacs.org.
[gmx-users] Number of urea molecules for 2.1 M solution
Dear all, How to calculate number of urea molecules required for a box size of 294.68 nm^3 for 2.1 M urea solution regds Divya -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Installation Problem... No command 'gmx' found
Hi, Try gmx [command] . Ex. gmx mdrun -option Regards, Husen > On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote: > > Hi, > > Try gmx_mpi. > > Regards > Terry > > >> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir >>wrote: >> >> Dear all user >> >> I install gromacs in my laptop its perfectly ok. But i have problem to >> install in my desktop there i face problem. >> In my desktop i want to compile with cuda accelerator and MPI option. I >> install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all >> this driver is ok. >> >> For gromacs i run this installation command. >> >> tar -xzvf gromacs-5.1.2.tar.gz >> cd gromacs-5.1.2.tar.gz >> mkdir build >> cd build >> CMAKE -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on >> -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on >> make -j16 >> make check >> sudo make install -j16 >> >> source /usr/local/gromacs/bin/GMXRC >> >> In the installation procedure i dont find any error. All 26 test completed >> without error. >> >> But when i try to run "gmx or gmx help" >> >> There is error no command gmx found. I need your guidance. >> >> Best Regards >> >> -- >> *Md Imrul Reza Shishir* >> -- >> 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 gmx-users-requ...@gromacs.org. > -- > 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 gmx-users-requ...@gromacs.org. -- 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 gmx-users-requ...@gromacs.org.