[gmx-users] Atomistic Simulation
Hello to everybody, I am new in atomistic simulations and a have some doubts about how to do it. I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane. My questions are, ¿Where do I get the pdb files of these molecules from? and ¿How do I know which force field I should choose in pdb2gmx in order to make the itp file? Thanks in advance, Panzu -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Assertion error
Dear Gromacs users, I am using Gromacs in a computer cluster using many processors (currently 228). Sometimes I get the following assertion error: *Assertion `timerq-cursor = current_time' failed at mxm/util/timerq.c:91* This error presents at some time inside of the simulation, every run at a different time, sometimes not at all, and is more frequent the more processors I try to use. The command I am using is: *mdrun_plumed -quiet -pd -s q60Bemd.tpr -o q60Bemd.trr -e q60Bemd.edr -g q60Bemd.log -c q60Bemd.gro -cpi state.cpt -multi 6 -replex 12500 -plumed plumed -maxh 7.5* Do you recognize the error? Any help will be appreciated. Thank you for your help. Yours, A. Gomez-Sicilia Protein nanomechanics lab Cajal Institute - CSIC Avda. Doctor Arce, 37 28002 Madrid (Spain) Phone number: (+34) 91-585.47.44 Fax number: (+34) 91-585.47.54 E-mail: agomezsici...@cajal.csic.es -- 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] Atomistic Simulation
I've just started doing atomistic simulations over the last few weeks as well and can share what I've learned so far. I have been using 'automated topology builder'. It only uses the gromos 53a6 forcefield so eliminates the choice if you want to use it. ATB generates the pdb and itp files for you. There are a lot of molecules already on there or you can submit you're own using a java script molecule builder. There may well be other ways to do this but I haven't found them yet. On 3 Dec 2013 10:14, panzu sergio.panzu...@estudiante.uam.es wrote: Hello to everybody, I am new in atomistic simulations and a have some doubts about how to do it. I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane. My questions are, ¿Where do I get the pdb files of these molecules from? and ¿How do I know which force field I should choose in pdb2gmx in order to make the itp file? Thanks in advance, Panzu -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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. - Sunday Times Scottish University of the Year 2011-2013 Top in the UK for student experience Fourth university in the UK and top in Scotland (National Student Survey 2012) We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] Atomistic Simulation
On 12/3/13 6:17 AM, Hardy, Adam wrote: I've just started doing atomistic simulations over the last few weeks as well and can share what I've learned so far. I have been using 'automated topology builder'. It only uses the gromos 53a6 forcefield so eliminates the choice if you want to use it. ATB generates the pdb and itp files for you. There are a lot of molecules already on there or you can submit you're own using a java script molecule builder. There may well be other ways to do this but I haven't found them yet. There are many other sources of parameters for simple molecules like these. 1. http://virtualchemistry.org/ 2. https://www.paramchem.org/ 3. AmberTools can be used to build (using xLeap) and create topologies (antechamber) for just about anything under GAFF There are plenty of other sources. The most important choice is constructing a model that accurately reproduces quantities of interest. It may take several attempts using several force fields to find the right one, or you may have to derive your own model from scratch if none of the existing ones is sufficient. On 3 Dec 2013 10:14, panzu sergio.panzu...@estudiante.uam.es wrote: Hello to everybody, I am new in atomistic simulations and a have some doubts about how to do it. I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane. My questions are, ¿Where do I get the pdb files of these molecules from? and ¿How do I know which force field I should choose in pdb2gmx in order to make the itp file? You don't need pdb2gmx at all here. The topology should be manually constructed; pdb2gmx is not useful in cases like these. -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 == -- 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] heating
It is an interesting question, because how does one generate velocities at 0 K? Random sampling from a Maxwellian distribution with mean zero and zero width :) At the end of the first step all velocities will be scaled to zero. That shouldn't be very unstable. Cheers, Tsjerk -- 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] Using several cores for MD production
Dear Users, I am using a cluster of 64 cores to perform my MD simulations using GROMACS version 4.5.5. I would be glad to know the exact mdrun command that will allow me use the available resources. Thank you. *Do all the good you can, By all the means you can, In all the ways you can, In all the places you can,At all the times you can,To all the people you can,As long as ever you can. - John Wesley. * -- 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] Using several cores for MD production
On 12/3/13 10:23 AM, MUSYOKA THOMMAS wrote: Dear Users, I am using a cluster of 64 cores to perform my MD simulations using GROMACS version 4.5.5. I would be glad to know the exact mdrun command that will allow me use the available resources. The answer depends entirely on the architecture of the cluster. Your sys admin should know. -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 == -- 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] Using several cores for MD production
Dear Justin, Well it seems i am the first one to do MD simulations in my lab and i am using a chemistry department cluster and nobody has prior knowledge on GROMACS. I can use all the cores in the cluster but need to know if there is a specific mdrun command that can allow me specify the number of cores to be used for the MD run. Thank you On Tue, Dec 3, 2013 at 5:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/3/13 10:23 AM, MUSYOKA THOMMAS wrote: Dear Users, I am using a cluster of 64 cores to perform my MD simulations using GROMACS version 4.5.5. I would be glad to know the exact mdrun command that will allow me use the available resources. The answer depends entirely on the architecture of the cluster. Your sys admin should know. -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 == -- 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. -- *MUSYOKA THOMMAS MUTEMIMob nos **+27844846540* *B.Sc Biochemistry (Kenyatta University), MSc Pharmaceutical Science (Nagasaki University)* *PhD Student - Research Unit in Bioinformatics (RUBi - Rhodes University)*Skype ID- MUSYOKA THOMMAS MUTEMI Alternative email - thom...@sia.co.ke *Do all the good you can, By all the means you can, In all the ways you can, In all the places you can,At all the times you can,To all the people you can,As long as ever you can. - John Wesley. * -- 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] virtual Site + verlet cuttoff problem
I am having difficulty running a simulation with virtual particles. If I use the group cutoff-scheme, the simulation runs, but if I use Verlet cutoff, i get the error The mass of a vsiten constructing atom is = 0. Does Verlet cutoff scheme not work with virtual particles, or is there some trick around this? Thanks, Brad -- View this message in context: http://gromacs.5086.x6.nabble.com/virtual-Site-verlet-cuttoff-problem-tp5013000.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Amber to Gromacs conversion
Hello Everyone, ambconv.tgz ( http://www.gromacs.org/Downloads/User_contributions/Other_software) tool exists for converting Amer input files into the ones for Gromacs. Now, it's README-eng file says that two Amber input files ( .atop (topology) and .rst (coordinates) ) are needed to generate input files for Gromacs. Corresponding file formats in current Amber version are .prmtop and .inpcrd respectively. Are these formats, just like older ones, exactly compatible with this tool? If not, are there other tools to convert Amber input files into the ones for Gromacs? If this tool can be used, is the condition of removing all water before applying this tool mandatory? Thank you. regards Chetan -- 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] Amber to Gromacs conversion
On 12/03/2013 11:45 AM, Chetan Mahajan wrote: are there other tools to convert Amber input files into the ones for Gromacs? I've had success with acpype: https://code.google.com/p/acpype/ Use the amb2gmx mode: acpype -p _prmtop_ -x _inpcrd_ -- Wes Barnett | jbarn...@tulane.edu -- 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] constraint in Production
Dear Users I have a problem about production step in MD simulation. Can this step be run with constraints or unconstraints? Best Regards -- 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] Virtual Sites
Hi, I haven't tried it but it should work if you set verlet-buffer-drift=-1 and set rlist manually. Roland On Mon, Dec 2, 2013 at 3:20 PM, Brad Van Oosten bv0...@brocku.ca wrote: I am trying to add virtual sites to a simulation with no mass or charge, just to make tracking the center of mass of groups later easier later on. However, I keep getting the warning The mass of a vsiten constructing atom is = 0 when i run grompp. Here's the section of my .itp file where i have defined them: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 CHX rtp CHX q 0.0 1 CLAL 1CHXCL1 1 -0.151 35.453 ; qtot -0.151 . . . . 63 CA 1CHXCZ2 63 0.083 12.011 ; qtot 0.144 64 CLAL 1CHXCL2 64 -0.144 35.453 ; qtot 0 65 MCH3 1CHX V1 65 0 0 ; 66 MCH3 1CHX V2 66 0 0 ; 67 MCH3 1CHX V3 67 0 0 ; 68 MCH3 1CHX V4 68 0 0 ; 69 MCH3 1CHX V5 69 0 0 ; 70 MCH3 1CHX V6 70 0 0 ; 71 MCH3 1CHX V7 71 0 0 ; 72 MCH3 1CHX V8 72 0 0 ; 73 MCH3 1CHX V9 73 0 0 ; 74 MCH3 1CHXV10 74 0 0 ; 75 MCH3 1CHXV11 75 0 0 ; 76 MCH3 1CHXV12 76 0 0 ; [virtual_sitesn] 65 2 8 9 10 11 66 2 2 3 6 7 67 2 1 4 5 12 13 68 2 14 15 16 17 18 69 2 19 20 21 22 23 70 2 24 25 26 27 28 29 30 31 32 71 2 33 34 35 36 37 38 39 40 41 72 2 49 50 51 52 53 73 2 44 45 46 47 48 74 2 42 43 54 57 58 75 2 55 56 59 60 76 2 61 62 63 64 Am I defining something wrong here? -- View this message in context: http://gromacs.5086.x6.nabble.com/Virtual-Sites-tp5012975.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Using several cores for MD production
The invocation line depends on the MPI tool installed on the cluster. E.g. in case of openmpi, you write openmpi -np 64 mdrun -dd 4 4 4 Dr. Vitaly V. Chaban On Tue, Dec 3, 2013 at 4:58 PM, MUSYOKA THOMMAS mutemibiochemis...@gmail.com wrote: Dear Justin, Well it seems i am the first one to do MD simulations in my lab and i am using a chemistry department cluster and nobody has prior knowledge on GROMACS. I can use all the cores in the cluster but need to know if there is a specific mdrun command that can allow me specify the number of cores to be used for the MD run. Thank you On Tue, Dec 3, 2013 at 5:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/3/13 10:23 AM, MUSYOKA THOMMAS wrote: Dear Users, I am using a cluster of 64 cores to perform my MD simulations using GROMACS version 4.5.5. I would be glad to know the exact mdrun command that will allow me use the available resources. The answer depends entirely on the architecture of the cluster. Your sys admin should know. -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 == -- 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. -- *MUSYOKA THOMMAS MUTEMIMob nos **+27844846540* *B.Sc Biochemistry (Kenyatta University), MSc Pharmaceutical Science (Nagasaki University)* *PhD Student - Research Unit in Bioinformatics (RUBi - Rhodes University)*Skype ID- MUSYOKA THOMMAS MUTEMI Alternative email - thom...@sia.co.ke *Do all the good you can, By all the means you can, In all the ways you can, In all the places you can,At all the times you can,To all the people you can,As long as ever you can. - John Wesley. * -- 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] Bug #554: pdb2gmx proton naming compliancy
Dear Users, does anyone know what was the resolution of this bug? http://redmine.gromacs.org/issues/554 How does one handle pdb2gmx with PDB files and avoid errors like this? Atom HB3 in residue ASP 2 was not found in rtp entry ASP with 14 atoms while sorting atoms. Thanks Mikhail Mikhail Kibalchenko, PhD mkibalche...@mednet.ucla.edumailto:mkibalche...@mednet.ucla.edu Postdoctoral Scholar, Neurology David Geffen School of Medicine at UCLA IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. -- 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] Amber to Gromacs conversion
THis looks interesting, However, any version is giving following error on test mentioned in README: ../acpype.py -i FFF.pdb File ../acpype.py, line 1231 with open(pklFile, wb) as f: # for python 2.6 or higher ^ SyntaxError: invalid syntax Unfortunately, I do not know python. Thanks Chetan On Tue, Dec 3, 2013 at 12:01 PM, Barnett, James W. jbarn...@tulane.eduwrote: On 12/03/2013 11:45 AM, Chetan Mahajan wrote: are there other tools to convert Amber input files into the ones for Gromacs? I've had success with acpype: https://code.google.com/p/acpype/ Use the amb2gmx mode: acpype -p _prmtop_ -x _inpcrd_ -- Wes Barnett | jbarn...@tulane.edu -- 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] Amber to Gromacs conversion
THis looks interesting, However, any version is giving following error on test mentioned in README: ../acpype.py -i FFF.pdb File ../acpype.py, line 1231 with open(pklFile, wb) as f: # for python 2.6 or higher ^ SyntaxError: invalid syntax Unfortunately, I do not know python. Thanks On Tue, Dec 3, 2013 at 12:01 PM, Barnett, James W. jbarn...@tulane.eduwrote: On 12/03/2013 11:45 AM, Chetan Mahajan wrote: are there other tools to convert Amber input files into the ones for Gromacs? I've had success with acpype: https://code.google.com/p/acpype/ Use the amb2gmx mode: acpype -p _prmtop_ -x _inpcrd_ -- Wes Barnett | jbarn...@tulane.edu -- 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] Amber to Gromacs conversion
You shouldn't change any of the code unless you know what you're doing. If you remove lines it will not work as intended. I think you simply need to upgrade your version of Python 2, according to the error message. jbarn...@tulane.edu | from mobile Chetan Mahajan chetanv...@gmail.com wrote: I did play around lines 1231 and 1232, by keeping 1232, while removing 1231, etc etc. No success so far! On Tue, Dec 3, 2013 at 5:17 PM, Chetan Mahajan chetanv...@gmail.com wrote: THis looks interesting, However, any version is giving following error on test mentioned in README: ../acpype.py -i FFF.pdb File ../acpype.py, line 1231 with open(pklFile, wb) as f: # for python 2.6 or higher ^ SyntaxError: invalid syntax Unfortunately, I do not know python. Thanks On Tue, Dec 3, 2013 at 12:01 PM, Barnett, James W. jbarn...@tulane.eduwrote: On 12/03/2013 11:45 AM, Chetan Mahajan wrote: are there other tools to convert Amber input files into the ones for Gromacs? I've had success with acpype: https://code.google.com/p/acpype/ Use the amb2gmx mode: acpype -p _prmtop_ -x _inpcrd_ -- Wes Barnett | jbarn...@tulane.edu -- 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] Amber to Gromacs conversion
Thanks, James. I already have python 2.4. regards Chetan On Tue, Dec 3, 2013 at 8:45 PM, Barnett, James W. jbarn...@tulane.eduwrote: You shouldn't change any of the code unless you know what you're doing. If you remove lines it will not work as intended. I think you simply need to upgrade your version of Python 2, according to the error message. jbarn...@tulane.edu | from mobile Chetan Mahajan chetanv...@gmail.com wrote: I did play around lines 1231 and 1232, by keeping 1232, while removing 1231, etc etc. No success so far! On Tue, Dec 3, 2013 at 5:17 PM, Chetan Mahajan chetanv...@gmail.com wrote: THis looks interesting, However, any version is giving following error on test mentioned in README: ../acpype.py -i FFF.pdb File ../acpype.py, line 1231 with open(pklFile, wb) as f: # for python 2.6 or higher ^ SyntaxError: invalid syntax Unfortunately, I do not know python. Thanks On Tue, Dec 3, 2013 at 12:01 PM, Barnett, James W. jbarn...@tulane.edu wrote: On 12/03/2013 11:45 AM, Chetan Mahajan wrote: are there other tools to convert Amber input files into the ones for Gromacs? I've had success with acpype: https://code.google.com/p/acpype/ Use the amb2gmx mode: acpype -p _prmtop_ -x _inpcrd_ -- Wes Barnett | jbarn...@tulane.edu -- 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] out of disk space error
hi chandan.. output for ls -1 is as follows: the directory from where i am running simulatons is in desktop .. and i have all the permissions for it. i am not that used to ubuntu and your suggestion will be of great help .. total 52 drwxrwxrwx 9 vansh vansh 4096 Nov 22 14:40 Desktop drwxr-xr-x 2 vansh vansh 4096 Nov 26 15:13 Documents drwxr-xr-x 8 vansh vansh 4096 Dec 3 16:43 Downloads -rw-r--r-- 1 vansh vansh 8445 Nov 12 10:03 examples.desktop -rw-rw-r-- 1 vansh vansh 5083 Dec 3 11:20 md.log drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Music drwxr-xr-x 2 vansh vansh 4096 Nov 13 22:49 Pictures drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Public drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Templates drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Videos - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013023.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] REMD
Sir, I want to do an REMD simulation having 16 replicas. But I have only 8 processors. Is it possible to do 16 replicas in 8 processors? How I can do this? -- 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] out of disk space error
Dear vaani, Please rerun the gmx executable. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Dec 4, 2013 at 11:20 AM, vaani vsha...@imtech.res.in wrote: hi chandan.. output for ls -1 is as follows: the directory from where i am running simulatons is in desktop .. and i have all the permissions for it. i am not that used to ubuntu and your suggestion will be of great help .. total 52 drwxrwxrwx 9 vansh vansh 4096 Nov 22 14:40 Desktop drwxr-xr-x 2 vansh vansh 4096 Nov 26 15:13 Documents drwxr-xr-x 8 vansh vansh 4096 Dec 3 16:43 Downloads -rw-r--r-- 1 vansh vansh 8445 Nov 12 10:03 examples.desktop -rw-rw-r-- 1 vansh vansh 5083 Dec 3 11:20 md.log drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Music drwxr-xr-x 2 vansh vansh 4096 Nov 13 22:49 Pictures drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Public drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Templates drwxr-xr-x 2 vansh vansh 4096 Nov 12 10:08 Videos - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013023.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] out of disk space error
Dear vaani, Sorry for the unclear message. Try running the mdrun command once again and post the out put of the log file. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Dec 4, 2013 at 12:34 PM, vaani vsha...@imtech.res.in wrote: i am sorry ..but i kind of dint get you .. - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013027.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] out of disk space error
sure .. - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013029.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Updating GTX670 PCIE speed from 5GT/s to 8GT/s resulted in about 10% speedup of md_run.
Below information might be of interest to the Gromacs development/optimization team. What can we derive from the 10% md_run speedup when PCIE3.0 speed increases from 5GT/s-8GT/s? A 60% PCIE speed increase results in a 10% run time reduction. Hence about 10/60=17% of the run time gets spent in (non-overlapping) PCIE bus communication for this particular configuration and for this particular simulated molecular system. I'm refering to the non-overlapping part as this is the part that is not hidden by (not overlapped with) calculations. So changing the PCIE speed provides a (non-user-friendly) knob to the gromacs developers to estimate the part of the run time that is determined by the (non-overlapping) PCIE bus communication. Not sure whether the Nvidia CUDA profiling environment provides a better way to quantify this. In case there isn't a better way, above method is a poor man's flow (for which you likely need root access) to provide this quantification. -- Henk Neefs Gromacs user -- View this message in context: http://gromacs.5086.x6.nabble.com/Updating-GTX670-PCIE-speed-from-5GT-s-to-8GT-s-resulted-in-about-10-speedup-of-md-run-tp5012945p5013031.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] out of disk space error
vaani wrote nvt.log http://gromacs.5086.x6.nabble.com/file/n5013030/nvt.log find the attached nvt.log file .. i have been equilibrating for 200ps in this example..and getting this error , but when equilibrating for 100ps there is no such error ..in later case i am getting this error at the time of 10 ns dynamic run - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/out-of-disk-space-error-tp5013021p5013032.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
