Re: [gmx-users] Giving an initial velocity to a group of atoms
Hi, You can use grompp to generate velocities, use editconf to turn the .tpr into a .gro file, and then do some operation on the velocities (e.g. add constants to various groups) but this won't help much in the condensed phase, because of collisions. Pulling groups is a different matter - see manual and tutorials. Mark On Sun, May 17, 2015 at 5:43 PM Jashimuddin Ashraf jashimuddin.ashra...@gmail.com wrote: Thanks a lot for your reply Dr. Lemkul. It is working now. The velocities are matching exactly as I have given them in the .gro file. But as the velocities I am giving are not very well calculated, the results are not very useful. If i wanted to give a group of atoms a certain velocity with respect to another group of atoms in my system (for example, if i had a system with a protein and a CNT and I wanted to start the simulation with an initial velocity of the CNT with respect to the protein) what shoud I do? I understand that this is not an error related to GROMACS but it would be very much helpful for me if you could shed some light on the problem that I am facing. Thanks in advance. On Thu, May 14, 2015 at 10:43 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/14/15 9:12 AM, Jashimuddin Ashraf wrote: Please ignore my previous message. Thanks again for your reply Dr. Lemkul. My files are uploaded here. https://drive.google.com/file/d/0B8p1k0KkNddyVXg4UDhyNmE5Njg/view?usp=sharing You're generating velocities (gen_vel = yes). That completely defeats the purpose of specifying velocities. Also note that using a finite cutoff for Coulombic interactions is not generally sound. -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. -- 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] freezegrps changing coordinates in NPT simulations
Hi Jon, I note that when using pcoupl = Parrinello-Rahman, the frozen group will be scaled. But when pcoupl = berendsen, the frozen group will stay at its initial position, and will not be scaled. Xuechuan At 2015-05-15 01:57:10, jwill...@andrew.cmu.edu wrote: Hello again, I'm running a simulation with graphene as a periodic molecule. I've frozen the carbons in place in the mdp file using: freezegrps = CG_CE freezedim= Y Y Y but when I run an NPT simulation, the entire system shrinks (including moving the carbons closer together) until it crashes. Everything works fine for NVT and minimization. Are there any tricks to freezing groups in NPT simulations? I've also attached my mdp file. Thank you! Jon -- 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] warter freeze into ice when cutoff-scheme=Verlet and coulombtype = cut-off
Hi everyone, I found that after gromacs version 4.6, when set cutoff-scheme=Verlet and coulombtype= cut-off, the waters in the system will freeze into ice. I known that charge-groups are necessary when using plain cut-off electrostatics. But I'm surprised that why the waters freeze into ice when using plain cut-off electrostatics without charge-groups? Could someone explain how it happenes? My mdp files are like this: integrator = md constraints = all_bonds dt = 0.002 nsteps = 5000 comm-mode =None nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 25000 nstxtcout= 500 xtc-precision= 1000 energygrps = MOL SOL nstlist = 1 ns_type = grid pbc = xyz rlist= 1.0 coulombtype = cut-off rcoulomb-switch = 0 rcoulomb = 1.0 vdw-type = cut-off rvdw-switch = 0 rvdw = 1.0 Tcoupl = V-rescale nsttcouple = -1 tc-grps = MOLSOL tau_t= 0.10.1 ref_t= 300 300 freezegrps = MOL freezedim= Y Y Y Thanks! Xuechuan -- 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] Carbon Nanotube `Y-Junctions'
The only software I am aware of that can do this out of the box is Nanotube Modeler: http://jcrystal.com/products/wincnt/ It is a paid product full of less than obvious bugs, but for the most part it works. The free demo will let you see the structures it generates, but you won't be able to export anything. Alex On Thu, May 14, 2015 at 10:35 PM, saeed poorasad s_poora...@yahoo.com wrote: Dear Gromacs users , Greetings .I am looking for XYZ or PDB file of Carbon nanotube ' Y-junction' . I will be grateful if you can let me know how i can find or make it . Thanks in advance .Best ,Saeed. -- 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] no output for rmsd-dist.xvg in g_rms
Dear GROMACS users, I am trying to calculate the file rmsd-dist.xvg using g_rms and GROMACS 5.0.4 g_rms -s ../minimizado.tpr -f ../production_300K_vac_all_fit.xtc -o rmsd.xvg -dist rmsd-dist.xvg However, any file is generated with that option, only rmsd.xvg. Is is maybe a bug, or how could I generate this file using g_rms? Best wishes, Rebeca Dr. Rebeca Garcia Santiago de Compostela University Spain -- 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 in UBUNTU
Dear all I followed the same steps to install Gromacs - 5.0.4 in ubuntu - 14.04 (64bit) and seems like things get installed but I am not able to get gmx solvant command. I have searched in my installation dir /soft/gmx504/bin/ and also source /soft/gmx504/bin/GMXRC.bash in my bashrc file. Kindly help. with regards Sanchaita On 14 May 2015 at 08:54, James Lord jjamesgreen...@gmail.com wrote: Hi Saeed, You don't necessarily need to install it first from Ubuntu software center and then update it. you can directly get the latest version and follow the instruction on gromacs website. Quick and dirty installation http://www.gromacs.org/Documentation/Installation_Instructions_5.0?highlight=command#TOC 1. Get the latest version of your C and C++ compilers. 2. Check that you have CMake version 2.8.8 or later. 3. Get and unpack the latest version of the GROMACS tarball. 4. Make a separate build directory and change to it. 5. Run cmake with the path to the source as an argument 6. Run make, make check, and make install Or, as a sequence of commands to execute: tar xfz gromacs-5.0.5.tar.gz cd gromacs-5.0.5 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC Cheers James On Thu, May 14, 2015 at 1:53 PM, saeed poorasad s_poora...@yahoo.com wrote: Dear Gromacs users , Greetings .I want to install Gromacs with using of UBUNTU software center . Now I want to know about updating process of this version of gromacs . Does it update automatically with Ubuntu ? Thanks for your attention .Best,Saeed. -- 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] question
Dear Justin Thanks for your answer. At first, I installed cmake 2.8.8 on centOS, by following commands: ./bootstrap; gmake; make install Then I used *Quick and dirty *installation http://www.gromacs.org/Documentation/Installation_Instructions_5.0?highlight=installation#TOC instruction. When I used cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON I encountered with: [root@lbm build]# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at least version 4.0) -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2 Downloading: http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz -- [download 100% complete] CMake Error at tests/CMakeLists.txt:57 (message): error: downloading ' http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz' failed status_code: 1 status_string: unsupported protocol log: About to connect() to gerrit.gromacs.org port 80 (#0) Trying 130.237.25.133... connected Connected to gerrit.gromacs.org (130.237.25.133) port 80 (#0) GET /download/regressiontests-5.0.5.tar.gz HTTP/1.1 Host: gerrit.gromacs.org Accept: */* HTTP/1.1 302 Found Date: Sun, 17 May 2015 14:37:01 GMT Server: Apache/2.2.22 (Ubuntu) Location: https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz Vary: Accept-Encoding Content-Length: 337 Content-Type: text/html; charset=iso-8859-1 Ignoring the response-body !DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN htmlhead title302 Found/title /headbody h1Found/h1 pThe document has moved a href= https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz;here/a./p hr addressApache/2.2.22 (Ubuntu) Server at gerrit.gromacs.org Port 80/address /body/html Connection #0 to host gerrit.gromacs.org left intact Issue another request to this URL: ' https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz' libcurl was built with SSL disabled, https: not supported! unsupported protocol Closing connection #0 -- Configuring incomplete, errors occurred! == What is wrong in my installation steps? Thanks in advance. -- 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] Simulation of Carbon Nanotubes with bending deformities
Dear gromacs users, I am simulating carbon nanotubes in GROMACS. So far I have only simulated straight CNTs. Now I'd also like to simulate CNTs with bending deformities. I have generated a bent .pdb of my nanotube structure and the simulation runs without any error (I have run the energy minimization and the structure after energy minimization is quite okay). But my problem is as soon as I run the simulation, the bent CNT goes straight within a few pico seconds. Is this because of my forcefield (I have only considered a bond length of 0.1418 nm in my forcefield.itp file)? How can I solve this problem? Thanks in advance. -- 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] RDF
Dear all, I want to calculate the radial distribution function of water molecules in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which is not logical I suppose. Is it meaningful if I separate oxygen and hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is reference atom necessary to get RDF? Thanks! -- 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] energy minimization error
On 5/16/15 11:35 PM, James Lord wrote: Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I do (redo) to resolve this issue? The bonds are defined in the topology. The DD algorithm reads what's in the coordinate file and builds cells based on the geometry it finds there. Without a full description of what's in your system, what steps you've taken to prepare it (full commands, in order), there's little I can suggest because it would all be guesswork. -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] question
On 5/16/15 11:49 PM, Andrew Bostick wrote: Dear Tsjerk I used pdb2gmx -f be_near.pdb -ignh -merge The error message from before said you were using version 4.5.3; the -merge option wasn't available in that version. Upgrade to something that's not ancient (preferably the latest version, 5.0.5) and it will work. -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] RDF
On 5/17/15 5:47 AM, mah maz wrote: Dear all, I want to calculate the radial distribution function of water molecules in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which is not logical I suppose. Is it meaningful if I separate oxygen and hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is reference atom necessary to get RDF? RDF is always calculated relative to a reference, but the default behavior is to consider all atom pairs; see the manual. It is generally standard practice in liquid RDF to separate out O-O vs. H-H etc. There is even an example figure of this in the manual. -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.
