[gmx-users] Gromacs 4.6.3 Installation Issues,
hi, i'm having difficulties installing gromacs by creating static links to the libraries for fftw3. i am currently running: cygwin1.7.24-1 cmake2.8.11.2-1 fftw33.3.3-1 this is the input that i'm attempting to utilize and flags errors (and some combination there of): cmake FFTW3F_INCLUDE_DIR=C:\FFTW\fftw-3.3.3\api FFTWF_LIBRARIES=C:\FFTW\fftw-3.3.3\.libs this is my error output: /cygdrive/c/gromacs/gromacs-4.6.3/build-cmake $ cmake FFTW3F_INCLUDE_DIR=C:\FFTW\fftw-3.3.3\api FFTWF_LIBRARIES=C:\FFTW\fftw-3.3.3\.libs .. -- Could NOT find CUDA (missing: CUDA_CUDART_LIBRARY) (found suitable version 5.5, minimum required is 3.2) -- Enabling native GPU acceleration CMake Error at cmake/FindFFTW.cmake:122 (message): The FFTW library /usr/local/lib/libfftw3f.a cannot be used with shared libraries. Provide a different FFTW library by setting FFTWF_LIBRARY. If you don't have a different one, recompile FFTW with --enable-shared or --with-pic. Or disable shared libraries for Gromacs by setting BUILD_SHARED_LIBS to no. Note: Disabling shared libraries requires up to 10x as much disk space. Call Stack (most recent call first): CMakeLists.txt:948 (find_package) any assistance would be appreciated. thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] 'Command not found' after installation
Hello all, I have been trying to get GROMACS (4.6.3) to work on my Mac (10.8.1). I downloaded the latest Intel C++ compilers and built Gromacs successfully (at least it appeared to be successful since I saw no error messages). I appended this line to my ~/.profile file: source /usr/local/gromacs/bin/GMXRC.bash, and restarted my terminal. Still, every time I type in a GROMACS command, such as luck, it says command not found. f I do echo $GMXDATA, it does return /usr/local/gromacs/share/gromacs, though. Thanks, John -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 'Command not found' after installation
Try g_luck. That's what has worked for me. On 08/24/2013 12:37 PM, Nimmy McNimmerson wrote: Hello all, I have been trying to get GROMACS (4.6.3) to work on my Mac (10.8.1). I downloaded the latest Intel C++ compilers and built Gromacs successfully (at least it appeared to be successful since I saw no error messages). I appended this line to my ~/.profile file: source /usr/local/gromacs/bin/GMXRC.bash, and restarted my terminal. Still, every time I type in a GROMACS command, such as luck, it says command not found. f I do echo $GMXDATA, it does return /usr/local/gromacs/share/gromacs, though. Thanks, John -- Wes Barnett | jbarn...@tulane.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] VDW Cut-off vs Switch with CHARMM force field
Hi! I am running explicit solvent simulations with the CHARMM force field implemented in gromacs 4.6.3. For VDW I have been using: rlist= 1.0 vdw-type = Cut-off rvdw = 1.0 in conjunction with PME and rcoulomb=1 for electrostatics. I wonder whether it would be more accurate to use instead a switching function for VDW between 0.8 and 1.0 and a larger rlist: rlist = 1.2 vdw-type= Switch rvdw_switch = 0.8 rvdw= 1.0 My question is: does switching between 0.8 and 1.0 generate less artifacts than abrupt truncation at 1.0 nm for VDW? Thanks! Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 'Command not found' after installation
Barnett, James W. jbarn...@tulane.edu wrote: Unfortunately this is now beyond what I know with a Mac. It sounds like a library is missing that GROMACS needs, or GROMACS can't find it, which is probably a simple fix. Perhaps someone more familiar with Mac will be able to weigh in. jbarn...@tulane.edu | from mobile-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] VDW Cut-off vs Switch with CHARMM force field
CHARMM is generally used with vdw switching between 1.0 and 1.2 nm - I presume it must be more accurate that way. There are a number of discussions on this already. Justin recommended using rlistlong 1.4 as well I think. You might want to use a short range cutoff (rcoulomb) of 1.2 for PME as well. That is what was done in the Bjelkmar et al paper where CHARMM27 was implemented in GROMACS (http://pubs.acs.org/doi/full/10.1021/ct900549r). Best wishes James On 24 Aug 2013, at 23:08, Gianluca Interlandi gianl...@u.washington.edu wrote: Hi! I am running explicit solvent simulations with the CHARMM force field implemented in gromacs 4.6.3. For VDW I have been using: rlist= 1.0 vdw-type = Cut-off rvdw = 1.0 in conjunction with PME and rcoulomb=1 for electrostatics. I wonder whether it would be more accurate to use instead a switching function for VDW between 0.8 and 1.0 and a larger rlist: rlist = 1.2 vdw-type= Switch rvdw_switch = 0.8 rvdw= 1.0 My question is: does switching between 0.8 and 1.0 generate less artifacts than abrupt truncation at 1.0 nm for VDW? Thanks! Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] VDW Cut-off vs Switch with CHARMM force field
Here is a relevant previous discussion http://lists.gromacs.org/pipermail/gmx-users/2013-May/081425.html Best wishes James On 25 Aug 2013, at 00:28, James Krieger jkrie...@mrc-lmb.cam.ac.uk wrote: CHARMM is generally used with vdw switching between 1.0 and 1.2 nm - I presume it must be more accurate that way. There are a number of discussions on this already. Justin recommended using rlistlong 1.4 as well I think. You might want to use a short range cutoff (rcoulomb) of 1.2 for PME as well. That is what was done in the Bjelkmar et al paper where CHARMM27 was implemented in GROMACS (http://pubs.acs.org/doi/full/10.1021/ct900549r). Best wishes James On 24 Aug 2013, at 23:08, Gianluca Interlandi gianl...@u.washington.edu wrote: Hi! I am running explicit solvent simulations with the CHARMM force field implemented in gromacs 4.6.3. For VDW I have been using: rlist= 1.0 vdw-type = Cut-off rvdw = 1.0 in conjunction with PME and rcoulomb=1 for electrostatics. I wonder whether it would be more accurate to use instead a switching function for VDW between 0.8 and 1.0 and a larger rlist: rlist = 1.2 vdw-type= Switch rvdw_switch = 0.8 rvdw= 1.0 My question is: does switching between 0.8 and 1.0 generate less artifacts than abrupt truncation at 1.0 nm for VDW? Thanks! Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] VDW Cut-off vs Switch with CHARMM force field
Thanks James! I was also wondering whether there is a significant penalty in performance if I use rlist=1.2 instead of rlist=1.0 There has already been a discussion in the NAMD mailing list about the VDW cutoff issue: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7551.html It is apparently common among NAMD users to use switch for VDW between 0.8 and 1.0 nm. I have often received negative criticism from supercomputer grant reviewers whenever I suggested using a 1.0 - 1.2 switching distance for VDW and 1.2 nm for Coulomb as in their eyes a 1.0 cutoff distance is enough (when PME is in use). Thanks! Gianluca On Sun, 25 Aug 2013, James Krieger wrote: Here is a relevant previous discussion http://lists.gromacs.org/pipermail/gmx-users/2013-May/081425.html Best wishes James On 25 Aug 2013, at 00:28, James Krieger jkrie...@mrc-lmb.cam.ac.uk wrote: CHARMM is generally used with vdw switching between 1.0 and 1.2 nm - I presume it must be more accurate that way. There are a number of discussions on this already. Justin recommended using rlistlong 1.4 as well I think. You might want to use a short range cutoff (rcoulomb) of 1.2 for PME as well. That is what was done in the Bjelkmar et al paper where CHARMM27 was implemented in GROMACS (http://pubs.acs.org/doi/full/10.1021/ct900549r). Best wishes James On 24 Aug 2013, at 23:08, Gianluca Interlandi gianl...@u.washington.edu wrote: Hi! I am running explicit solvent simulations with the CHARMM force field implemented in gromacs 4.6.3. For VDW I have been using: rlist= 1.0 vdw-type = Cut-off rvdw = 1.0 in conjunction with PME and rcoulomb=1 for electrostatics. I wonder whether it would be more accurate to use instead a switching function for VDW between 0.8 and 1.0 and a larger rlist: rlist = 1.2 vdw-type= Switch rvdw_switch = 0.8 rvdw= 1.0 My question is: does switching between 0.8 and 1.0 generate less artifacts than abrupt truncation at 1.0 nm for VDW? Thanks! Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] VDW Cut-off vs Switch with CHARMM force field
On 8/24/13 8:19 PM, Gianluca Interlandi wrote: Thanks James! I was also wondering whether there is a significant penalty in performance if I use rlist=1.2 instead of rlist=1.0 I doubt one would consider it significant, but of course any time you decrease rlist, you potentially speed up the simulation a bit. Whether or not doing so is appropriate is an entirely separate issue. There has already been a discussion in the NAMD mailing list about the VDW cutoff issue: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7551.html It is apparently common among NAMD users to use switch for VDW between 0.8 and 1.0 nm. I have often received negative criticism from supercomputer grant reviewers whenever I suggested using a 1.0 - 1.2 switching distance for VDW and 1.2 nm for Coulomb as in their eyes a 1.0 cutoff distance is enough (when PME is in use). It is important to remember that all of these settings are interconnected. For PME, rlist must equal rcoulomb. It is true that the value of rcoulomb is somewhat flexible when using PME, but you must be sure that the changes you are making to other settings are not detrimental. If you decrease rcoulomb, then you must also decrease rlist, which then also has implications for van der Waals interactions, even if the change was originally only motivated by using PME. To reproduce the typical CHARMM usage, one would set: vdwtype = switch rlist = 1.2 rlistlong = 1.4 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 Unless you can demonstrate that your changes in cutoffs do not produce artifacts or lead to other inaccuracies using robust test systems, I wouldn't recommend any deviations. Note that the response you received on the NAMD list also suggested this to be true. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Help with Error Message
So I started following some tutorials online since I didn't get a response last time. the tutorial I'm using is: http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/ I followed that tutorial to the second page and got stuck at the step where it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh I picked GROMOS96 45a3 force field(11) for the force field and spc(1) for the water model but got the following error message: Opening force field file /usr/local/gromacs/share/gromacs/top/gromos45a3.ff/aminoacids.r2b Reading protein.pdb... --- Program pdb2gmx, VERSION 4.6.3 Source code file: /Users/christinalin/wget-1.14/gromacs-4.6.3/src/gmxlib/futil.c, line: 593 File input/output error: protein.pdb For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Help please? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help with Error Message
It sounds like you dont have the .pdb file in your working directory. Perhaps you need to learn a bit about unix filesystems On Sat, Aug 24, 2013 at 6:18 PM, The One And Only chappybo...@gmail.comwrote: So I started following some tutorials online since I didn't get a response last time. the tutorial I'm using is: http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/ I followed that tutorial to the second page and got stuck at the step where it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh I picked GROMOS96 45a3 force field(11) for the force field and spc(1) for the water model but got the following error message: Opening force field file /usr/local/gromacs/share/gromacs/top/gromos45a3.ff/aminoacids.r2b Reading protein.pdb... --- Program pdb2gmx, VERSION 4.6.3 Source code file: /Users/christinalin/wget-1.14/gromacs-4.6.3/src/gmxlib/futil.c, line: 593 File input/output error: protein.pdb For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Help please? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help with Error Message
that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in terms of getting help. Do you know how to get the right .pdb file in my working directory? On Sat, Aug 24, 2013 at 6:23 PM, Rafael I. Silverman y de la Vega rsilv...@ucsc.edu wrote: It sounds like you dont have the .pdb file in your working directory. Perhaps you need to learn a bit about unix filesystems On Sat, Aug 24, 2013 at 6:18 PM, The One And Only chappybo...@gmail.com wrote: So I started following some tutorials online since I didn't get a response last time. the tutorial I'm using is: http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/ I followed that tutorial to the second page and got stuck at the step where it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh I picked GROMOS96 45a3 force field(11) for the force field and spc(1) for the water model but got the following error message: Opening force field file /usr/local/gromacs/share/gromacs/top/gromos45a3.ff/aminoacids.r2b Reading protein.pdb... --- Program pdb2gmx, VERSION 4.6.3 Source code file: /Users/christinalin/wget-1.14/gromacs-4.6.3/src/gmxlib/futil.c, line: 593 File input/output error: protein.pdb For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Help please? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help with Error Message
On 8/24/13 9:26 PM, The One And Only wrote: that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in terms of getting help. Do you know how to get the right .pdb file in my working directory? Rudimentary Unix commands like cp and mv are covered in any Unix/Linux tutorial. Google can find lots of good ones. Producing a quality simulation cannot be rushed, and if you don't know the fundamentals of navigating the command line and directory structure, it's nearly impossible. You need to invest time in learning the environment before doing anything, I'm afraid. Just to give a bit of perspective, we used to train our undergrads for nearly a full semester (at least 2-3 months) before requiring them to do any real work. At least a week or two of that time was spent getting used to command line and Linux in general. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help with Error Message
so how do i solve the protein.pdb issue? On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/24/13 9:26 PM, The One And Only wrote: that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in terms of getting help. Do you know how to get the right .pdb file in my working directory? Rudimentary Unix commands like cp and mv are covered in any Unix/Linux tutorial. Google can find lots of good ones. Producing a quality simulation cannot be rushed, and if you don't know the fundamentals of navigating the command line and directory structure, it's nearly impossible. You need to invest time in learning the environment before doing anything, I'm afraid. Just to give a bit of perspective, we used to train our undergrads for nearly a full semester (at least 2-3 months) before requiring them to do any real work. At least a week or two of that time was spent getting used to command line and Linux in general. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help with Error Message
Never mind, I'm dumb. I just realized that protein.pdb means i have to specify which protein i want like 1qlz.pdb and not actually type protein.pdb BUT THANKS GUYS!! On Sat, Aug 24, 2013 at 6:40 PM, The One And Only chappybo...@gmail.comwrote: so how do i solve the protein.pdb issue? On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/24/13 9:26 PM, The One And Only wrote: that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in terms of getting help. Do you know how to get the right .pdb file in my working directory? Rudimentary Unix commands like cp and mv are covered in any Unix/Linux tutorial. Google can find lots of good ones. Producing a quality simulation cannot be rushed, and if you don't know the fundamentals of navigating the command line and directory structure, it's nearly impossible. You need to invest time in learning the environment before doing anything, I'm afraid. Just to give a bit of perspective, we used to train our undergrads for nearly a full semester (at least 2-3 months) before requiring them to do any real work. At least a week or two of that time was spent getting used to command line and Linux in general. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Ok now what?
I've been able to set up everything correctly according to the tutorial I found on the website. I got the following error when I typed: grompp -v -f minim.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o 1qlz-EM-solvated.tpr Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... processing topology... Generated 141 of the 1176 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file 1qlz.top, line 7226]: System has non-zero total charge: -2.99 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. processing coordinates... --- Program grompp, VERSION 4.6.3 Source code file: /Users/christinalin/wget-1.14/gromacs-4.6.3/src/kernel/grompp.c, line: 563 Fatal error: number of coordinates in coordinate file (1qlz-solvated.pdb, 24574) does not match topology (1qlz.top, 24672) I'm stuck. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Ok now what?
-Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of The One And Only Sent: Sunday, 25 August 2013 12:20 PM To: forum Subject: [gmx-users] Ok now what? I've been able to set up everything correctly according to the tutorial I found on the website. I got the following error when I typed: grompp -v -f minim.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o 1qlz-EM-solvated.tpr Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... processing topology... Generated 141 of the 1176 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file 1qlz.top, line 7226]: System has non-zero total charge: -2.99 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. processing coordinates... --- Program grompp, VERSION 4.6.3 Source code file: /Users/christinalin/wget-1.14/gromacs-4.6.3/src/kernel/grompp.c, line: 563 Fatal error: number of coordinates in coordinate file (1qlz-solvated.pdb, 24574) does not match topology (1qlz.top, 24672) Check your topology file and make sure that the number of atoms are correct. I guess in your topology you have more water SOL atoms than in your pdb file, so check that and amend it accordingly. As you are very new for this work it is obvious that you will face so many error, are you planning to post all those errors every time you get one :) As Justin suggested, better for you to invest time in learning with someone before doing anything. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] VDW Cut-off vs Switch with CHARMM force field
vdwtype = switch rlist = 1.2 rlistlong = 1.4 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 I'm confused about the difference between rlist and rlistlong. I am planning to also setup an implicit solvent simulation with GBSA and CHARMM-FF. Would this make sense? rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0 rcoulomb = 1.2 vdw-type = Switch rvdw_switch = 1.0 rvdw = 1.2 Thanks! Gianluca == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] rvdw, rlist and rcoulomb for Amber03
Hi Justin, In a recent post (http://gromacs.5086.x6.nabble.com/VDW-Cut-off-vs-Switch-with-CHARMM-force-field-td5010695.html;cid=1377399737789-944) you commented that: Unless you can demonstrate that your changes in cutoffs do not produce artifacts or lead to other inaccuracies using robust test systems, I wouldn't recommend any deviations. I have the habit of reading the original forcefield papers and using their parameters directly. In this regard, I use rlist=rvdw=rcoulomb=0.8 nm for Amber03 (same parameters are used in the following tutorial: http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2) ). My system is a protein in a water box with counter-ions and 0.1M NaCl. It is a NVT simulation at 310 K. My queries are the following 1) Are my parameters appropriate for Amber03? 2) How would I go about constructing robust test systems to demonstrate the validity of my parameters for a protein in a water box? What parameters do I measure? Energies? Any structural parameters in particular? Thank you. -- View this message in context: http://gromacs.5086.x6.nabble.com/rvdw-rlist-and-rcoulomb-for-Amber03-tp5010711.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] #coordinates do not match
I've tried the same process twice to two different proteins, but still got the same error that the #coordinates in the topology file did not match the #coordinates of the file I'm trying to use (1xyw-solvated.pdb). Below is the process I went through: *pdb2gmx -f 1xyw.pdb -o 1xyw.gro -p 1xyw.top -ignh* *grompp -f minim.mdp -c 1xyw.gro -p 1xyw.top -o 1xyw-EM-vacuum.tpr* *mdrun -v -deffnm 1xyw-EM-vacuum -c 1xyw-EM-vacuum.pdb -pd* *editconf -f 1xyw-EM-vacuum.pdb -o 1xyw-PBC.gro -bt dodecahedron -d 1.0* *genbox -cp 1xyw-PBC.gro -cs spc216.gro -p 1xyw.top -o 1xyw-water.pdb* *grompp -v -f minim.mdp -c 1xyw-water.pdb -p 1xyw.top -o 1xyw-water.tpr* *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname NA -nname CL* *grompp -v -f minim.mdp -c 1xyw-solvated.pdb -p 1xys.top -o 1xyw-EM-solvated.tpr* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] #coordinates do not match
Hi, In *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname NA -nname CL* , you have not used -p 1xys.top Consequently, I don't think the ions are written into your .top . Please check and see if grompp works. On Sun, Aug 25, 2013 at 9:34 AM, The One And Only chappybo...@gmail.comwrote: I've tried the same process twice to two different proteins, but still got the same error that the #coordinates in the topology file did not match the #coordinates of the file I'm trying to use (1xyw-solvated.pdb). Below is the process I went through: *pdb2gmx -f 1xyw.pdb -o 1xyw.gro -p 1xyw.top -ignh* *grompp -f minim.mdp -c 1xyw.gro -p 1xyw.top -o 1xyw-EM-vacuum.tpr* *mdrun -v -deffnm 1xyw-EM-vacuum -c 1xyw-EM-vacuum.pdb -pd* *editconf -f 1xyw-EM-vacuum.pdb -o 1xyw-PBC.gro -bt dodecahedron -d 1.0* *genbox -cp 1xyw-PBC.gro -cs spc216.gro -p 1xyw.top -o 1xyw-water.pdb* *grompp -v -f minim.mdp -c 1xyw-water.pdb -p 1xyw.top -o 1xyw-water.tpr* *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname NA -nname CL* *grompp -v -f minim.mdp -c 1xyw-solvated.pdb -p 1xys.top -o 1xyw-EM-solvated.tpr* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] #coordinates do not match
How do you decrease the number of solvent molecules in a topology file? I think this will solve my problem. On Sat, Aug 24, 2013 at 9:08 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi, In *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname NA -nname CL* , you have not used -p 1xys.top Consequently, I don't think the ions are written into your .top . Please check and see if grompp works. On Sun, Aug 25, 2013 at 9:34 AM, The One And Only chappybo...@gmail.com wrote: I've tried the same process twice to two different proteins, but still got the same error that the #coordinates in the topology file did not match the #coordinates of the file I'm trying to use (1xyw-solvated.pdb). Below is the process I went through: *pdb2gmx -f 1xyw.pdb -o 1xyw.gro -p 1xyw.top -ignh* *grompp -f minim.mdp -c 1xyw.gro -p 1xyw.top -o 1xyw-EM-vacuum.tpr* *mdrun -v -deffnm 1xyw-EM-vacuum -c 1xyw-EM-vacuum.pdb -pd* *editconf -f 1xyw-EM-vacuum.pdb -o 1xyw-PBC.gro -bt dodecahedron -d 1.0* *genbox -cp 1xyw-PBC.gro -cs spc216.gro -p 1xyw.top -o 1xyw-water.pdb* *grompp -v -f minim.mdp -c 1xyw-water.pdb -p 1xyw.top -o 1xyw-water.tpr* *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname NA -nname CL* *grompp -v -f minim.mdp -c 1xyw-solvated.pdb -p 1xys.top -o 1xyw-EM-solvated.tpr* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 'Command not found' after installation
Hi, Apparently this is an issue with my intel compiler; the dynamic linker isn't finding the libiomp5.dylib library. However, I don't know how to fix this (the google results haven't worked.) Please help, Thanks, John From: Barnett, James W. jbarn...@tulane.edu To: nimzs...@yahoo.com Sent: Saturday, August 24, 2013 3:07 PM Subject: Re: [gmx-users] 'Command not found' after installation Unfortunately this is now beyond what I know with a Mac. It sounds like a library is missing that GROMACS needs, or GROMACS can't find it, which is probably a simple fix. Perhaps someone more familiar with Mac will be able to weigh in. jbarn...@tulane.edu | from mobile nimzs...@yahoo.com wrote: This gives the following: dyld: Library not loaded: libiomp5.dylib Referenced from: /usr/local/gromacs/bin/g_luck Reason: image not found Trace/BPT trap: 5 If I try 'pdb2gmx', it says: dyld: Library not loaded: libiomp5.dylib Referenced from: /usr/local/gromacs/bin/pdb2gmx Reason: image not found Trace/BPT trap: 5 Did the installation not work properly? From: Barnett, James W. jbarn...@tulane.edu To: Nimmy McNimmerson nimzs...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, August 24, 2013 10:42 AM Subject: Re: [gmx-users] 'Command not found' after installation Try g_luck. That's what has worked for me. On 08/24/2013 12:37 PM, Nimmy McNimmerson wrote: Hello all, I have been trying to get GROMACS (4.6.3) to work on my Mac (10.8.1). I downloaded the latest Intel C++ compilers and built Gromacs successfully (at least it appeared to be successful since I saw no error messages). I appended this line to my ~/.profile file: source /usr/local/gromacs/bin/GMXRC.bash, and restarted my terminal. Still, every time I type in a GROMACS command, such as luck, it says command not found. f I do echo $GMXDATA, it does return /usr/local/gromacs/share/gromacs, though. Thanks, John -- Wes Barnett | jbarn...@tulane.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
