[gmx-users] Minimization-single or double precision
Dear Gromacs users, I wanted to know whether it is correct doing minimization in double precision and rest all - pdb2gmx, editconf, genbox, grompp and mdrun itself in single precision. I had got convergence during energy minimization using double precision but not single precision (input files for both were same and prepared using single precision). Thanks in advance MKS -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] Energy minimization - single/double precision
Dear Gromacs users, I wanted to know whether it is correct doing minimization in double precision and rest all - pdb2gmx, editconf, genbox, grompp and mdrun itself in single precision. I had got convergence during energy minimization using double precision but not single precision (input files for both were same and prepared using single precision). Thanks in advance MKS -- 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] Doubts regarding Simulation box
Dear Gromacs users, I am new to gromacs. I want to simulate a system (protein) with a dodecahedron box in order to minimize the time. rlist = rcolumb = 1.2nm; (PME) rvdw = 1.1nm; rvdw_switch = 0 (using vdwtype = switch) so while setting the simulation box, should i give the value of -d as =1.2nm? Does this same rule apply to a cubic box also? ie., irrespective of the box I use whether dodecahedron, cubic or octahedron, according to the cutoff (max (rlist, rvdw, rcoloumb)) I have to use -d as 1.2nm, or higher? Kindly anyone clarify my doubts Thanks in advance. -- 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] pdb2gmx: segmentation fault
Hi Tsjerk, Ya, it happened with other ff, too. My command line is pdb2gmx -ignh -f Sur.pdb i've browsed through the pdb file and it looks ok... joyce From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, January 13, 2011 15:31:35 Subject: Re: [gmx-users] pdb2gmx: segmentation fault Hi Joyce, Can you post the command line? Does it also happen with other force fields? Is there something notable about the pdb file? Cheers, Tsjerk On Jan 13, 2011 7:48 AM, Kwee Hong jestan1...@yahoo.com wrote: Hi Mark, I tried v 4.0.7 and 4.5.1. Both experiencing the same situation. The file is actually saved as pdb file from autodock output using pymol. Joyce From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, January 13, 2011 13:43:47 Subject: Re: [gmx-users] pdb2gmx: segmentation fault On 01/13/11, Kwee Hong jestan1...@yahoo.com wrote: Hi,I was trying to generate topolo... -- 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] Melting Temperatue
Hello, Experimentals often use heating to define strength of contacts. Has anyone tried to calculate this using MD/GROMACS or can anyone refer me to a work which was done on this subject? Thanks, Ifat M.Sc. Student Bar Ilan University Ramat Gan Israel -- 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] creating mdrun_mpi with cmake
Dear users: I have successfully compiled gromacs 4.5.3 with the description posted here: http://www.gromacs.org/Developer_Zone/Cmake#An_example_installation How do I compile the mpi version of mdrun? I tried simply adding openmpi libraries to my paths, but this was not enough. Is there a special cmake flag? I could not find on one the internet. Second, Do I even need to compile with mpi in gromacs 4.5.3? It seems to me that non-mpi mdrun can do this with threads (at least over cores on a single box). Thank you, Chris. -- 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] problem when calculating the solvation free energy of ARG in water using PME.
1. How sure are you that you have reproduced the run exactly on the different machines? 2. Are there any other differences besides machine? Number of cores? 3. What's your water model? 4. What else is in your system? (counterions?) 5. What are your crash/not-crash statistics? The OS difference might just be noise. I realize that this could be some machine-dependent error (as you seem to be suggesting) but I would not be able to help you with that. Let's ensure that it is not some other difference and then you could file a redmine issue if the problem can not be resolved. You likely have a good small test case. Chris. -- original message -- I am trying to calculate the solvation free energy of ARG in water, using GROMACS 4.0.7 (using TI). I found that when I run the calculations on linux machines (I try few) it run OK, but when I run the calculations on OSX it crashed in most lambda points. I run the calculations using PME and RF, and the problem is consisted only with PME. I also done the same thing for ALA and it works fine. So I guess it has a connection to the charges. Any advices? Best regards, -- 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] creating mdrun_mpi with cmake
chris.ne...@utoronto.ca wrote: Dear users: I have successfully compiled gromacs 4.5.3 with the description posted here: http://www.gromacs.org/Developer_Zone/Cmake#An_example_installation How do I compile the mpi version of mdrun? I tried simply adding openmpi libraries to my paths, but this was not enough. Is there a special cmake flag? I could not find on one the internet. -DGMX_MPI=ON Other relevant options may or may not include: -DGMX_DEFAULT_SUFFIX -DMPI_COMPILER -DMPI_INCLUDE_PATH I don't know what you've already found, but I've had to use all of these to get a proper mdrun with a custom suffix (with -DGMX_DEFAULT_SUFFIX=OFF). Second, Do I even need to compile with mpi in gromacs 4.5.3? It seems to me that non-mpi mdrun can do this with threads (at least over cores on a single box). That's my understanding, as well. -Justin Thank you, Chris. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Melting Temperatue
This one comes to mind: D. Paschek and A.E. Garcia, ?Reversible temperature and pressure denaturation of a protein fragment: Replica exchange molecular dynamics simulation study.? Phys. Rev. Let. 93: 238105 (2004) -- original message -- Hello, Experimentals often use heating to define strength of contacts. Has anyone tried to calculate this using MD/GROMACS or can anyone refer me to a work which was done on this subject? Thanks, Ifat M.Sc. Student Bar Ilan University -- 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] galactose
Hello, I am trying to simulate galactose in water using Gromos FFG53A6 force field. The molecular formula for galactose is C6H12O6, however in the FFG53A6.rtp file, the molecular formula is C6H10O5 for galactose-A and B. Why is it different? I would really appreciate some help! Thanks -Nisha P -- 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] galactose
nishap.pa...@utoronto.ca wrote: Hello, I am trying to simulate galactose in water using Gromos FFG53A6 force field. The molecular formula for galactose is C6H12O6, however in the FFG53A6.rtp file, the molecular formula is C6H10O5 for galactose-A and B. Why is it different? I would really appreciate some help! The Gromos96 sugar parameters assume the residues are part of a larger polymer, thus condensation of sugars eliminates the missing H2O. There is a newer version of these parameters that was recently published, which may have some relevant details: dx.doi.org/10.1002/jcc.21675 -Justin Thanks -Nisha P -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] galactose
Hello, I am trying to simulate galactose in water using Gromos FFG53A6 force field. The molecular formula for galactose is C6H12O6, however in the FFG53A6.rtp file, the molecular formula is C6H10O5 for galactose-A and B. Why is it different? I would really appreciate some help! Thanks -Nisha P -- 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] creating mdrun_mpi with cmake
Thanks for your help Justin. I have updated the instructions at: http://www.gromacs.org/Developer_Zone/Cmake#An_example_installation with what has worked for me. chris.neale at utoronto.ca wrote: Dear users: I have successfully compiled gromacs 4.5.3 with the description posted here: http://www.gromacs.org/Developer_Zone/Cmake#An_example_installation How do I compile the mpi version of mdrun? I tried simply adding openmpi libraries to my paths, but this was not enough. Is there a special cmake flag? I could not find on one the internet. -DGMX_MPI=ON Other relevant options may or may not include: -DGMX_DEFAULT_SUFFIX -DMPI_COMPILER -DMPI_INCLUDE_PATH I don't know what you've already found, but I've had to use all of these to get a proper mdrun with a custom suffix (with -DGMX_DEFAULT_SUFFIX=OFF). Second, Do I even need to compile with mpi in gromacs 4.5.3? It seems to me that non-mpi mdrun can do this with threads (at least over cores on a single box). That's my understanding, as well. -Justin Thank you, Chris. -- 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] galactose
Thanks. I am going to look over it. But I was wondering is it possible to just simulate one molecule of sucrose (glucose+fructose) in water using any of the force fields by Gromacs? I realize I would have to add the parameters to the .rtp files, but as you mentioned that the force fields recognizes them as part of the larger polymer and so it doesn't take into account the missing atoms. -Nisha P Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello, I am trying to simulate galactose in water using Gromos FFG53A6 force field. The molecular formula for galactose is C6H12O6, however in the FFG53A6.rtp file, the molecular formula is C6H10O5 for galactose-A and B. Why is it different? I would really appreciate some help! The Gromos96 sugar parameters assume the residues are part of a larger polymer, thus condensation of sugars eliminates the missing H2O. There is a newer version of these parameters that was recently published, which may have some relevant details: dx.doi.org/10.1002/jcc.21675 -Justin Thanks -Nisha P -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Installing multiple versions of GROMACS together? - program suffix
Hi, I am finally installing gmx 4.5.3 after a year and a half with 4.0.7 :) My issue is that I'd like to continue to keep both versions (there's stuff I need to analyze/continue etc. with previous version and I'd keep it for homogeneity and avoid issues), so I thought that configuring 4.5.3 with ./configure --with-fft=fftw3 --prefix=/home/ms872/software/bin --program-suffix=_453 would have been enough. However I double-checked nothing in the *tools* directory is compiled with the _453 suffix. I obviously don't want analysis tools to be overwritten. I suspect there's a more elegant solution than renaming by hand: what am I missing? Thanks! m. -- 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] Simulations on GPU
On Tue, Jan 4, 2011 at 3:17 PM, Rossen Apostolov ros...@kth.se wrote: On 1/4/11 3:16 PM, Francesco Oteri wrote: Maybe the used force-field is wrong. mdrun-gpu is able to use the AMBER forcefield, but it is not possible using gromos force-field. When gromos force-field is used, the output is full of NaN Is that the case? mdrun should complain and exit if the FF isn't supported. I get this error when I try to run mdrun-gpu with a forcefield that has GROMOS interaction types: Fatal error: OpenMM does not support (some) of the provided interaction type(s) (G96Angle). Maybe it's possible to run a short simulation on a small system and not encounter the missing interactions? I don't know enough about how the forcefields work to know whether that would get past the error. -Keith Rossen -- gmx-users mailing list gmx-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] galactose
nishap.pa...@utoronto.ca wrote: Thanks. I am going to look over it. But I was wondering is it possible to just simulate one molecule of sucrose (glucose+fructose) in water using any of the force fields by Gromacs? I realize I would have to add the parameters to the .rtp files, but as you mentioned that the force fields recognizes them as part of the larger polymer and so it doesn't take into account the missing atoms. You have to add the terminal atoms to the .rtp entries, that's all. -Justin -Nisha P Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello, I am trying to simulate galactose in water using Gromos FFG53A6 force field. The molecular formula for galactose is C6H12O6, however in the FFG53A6.rtp file, the molecular formula is C6H10O5 for galactose-A and B. Why is it different? I would really appreciate some help! The Gromos96 sugar parameters assume the residues are part of a larger polymer, thus condensation of sugars eliminates the missing H2O. There is a newer version of these parameters that was recently published, which may have some relevant details: dx.doi.org/10.1002/jcc.21675 -Justin Thanks -Nisha P -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Installing multiple versions of GROMACS together? - program suffix
devicerandom wrote: Hi, I am finally installing gmx 4.5.3 after a year and a half with 4.0.7 :) My issue is that I'd like to continue to keep both versions (there's stuff I need to analyze/continue etc. with previous version and I'd keep it for homogeneity and avoid issues), so I thought that configuring 4.5.3 with ./configure --with-fft=fftw3 --prefix=/home/ms872/software/bin --program-suffix=_453 would have been enough. However I double-checked nothing in the *tools* directory is compiled with the _453 suffix. I obviously don't want analysis tools to be overwritten. I suspect there's a more elegant solution than renaming by hand: what am I missing? Thanks! I can't replicate this; the same command works perfectly for me. Instead of installing in the same directory where there are existing executables, what happens if you try to install in a fresh directory? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Installing multiple versions of GROMACS together? - program suffix
On 13/01/11 21:01, Justin A. Lemkul wrote: ./configure --with-fft=fftw3 --prefix=/home/ms872/software/bin --program-suffix=_453 would have been enough. However I double-checked nothing in the *tools* directory is compiled with the _453 suffix. I obviously don't want analysis tools to be overwritten. I suspect there's a more elegant solution than renaming by hand: what am I missing? Thanks! I can't replicate this; the same command works perfectly for me. Just to be sure: does this mean you have anadock_453 , demux.pl_453 , do_dssp_453 etc. ? Instead of installing in the same directory where there are existing executables, what happens if you try to install in a fresh directory? Uhm, I don't get it - how installing in another directory could change their names? I still don't dare to type make install until I see g_hbond_453 instead of g_hbond, for example :) m. -- 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] TZD Tautomers
Hi All, I happened to find a published article where molecular docking simulations of TZDs against a novel protein is detailed: Structure-based design of a thiazolidinedione which targets the mitochondrial protein mitoNEET Bioorg Med Chem Lett. 2010 Feb 1;20(3):819-23 In this paper, the authors, using MarvinSketch v3.5.4, determined that the TZDs would exist predominantly in the enol form at pH 7.4, as opposed to the diketone form (see attached figure). It appears that the article's tautomer prediction was based only on the pH prior to docking, and had nothing to do with ligand-protein interactions. Does anyone know if the diketone or enol, or perhaps a different tautomer, would be predominant at pH 7.4? Thanks in advance. Nancy attachment: Pioglitazone_Tautomers.png-- 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] Installing multiple versions of GROMACS together? - program suffix
devicerandom wrote: On 13/01/11 21:01, Justin A. Lemkul wrote: ./configure --with-fft=fftw3 --prefix=/home/ms872/software/bin --program-suffix=_453 would have been enough. However I double-checked nothing in the *tools* directory is compiled with the _453 suffix. I obviously don't want analysis tools to be overwritten. I suspect there's a more elegant solution than renaming by hand: what am I missing? Thanks! I can't replicate this; the same command works perfectly for me. Just to be sure: does this mean you have anadock_453 , demux.pl_453 , do_dssp_453 etc. ? All except the .pl scripts (demux.pl and xplorgmx.pl), GMXRC*, and completion.*; they are not affected. Instead of installing in the same directory where there are existing executables, what happens if you try to install in a fresh directory? Uhm, I don't get it - how installing in another directory could change their names? I still don't dare to type make install until I see g_hbond_453 instead of g_hbond, for example :) I wanted to make sure you hadn't simply over-written existing executables, or that there was no strange (unexpected) conflict with installing to the same directory. If you're worried about what you're seeing assembled in the source tree vs. what's installed, don't. The binary built in the source tree is g_hbond, but will be installed as g_hbond_453: $ make install ... /bin/sh ../../libtool --mode=install /usr/bin/install -c g_hbond '/home/justin/gmx453/bin/./g_hbond_453' /usr/bin/install -c g_hbond /home/justin/gmx453/bin/./g_hbond_453 -Justin m. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Installing multiple versions of GROMACS together? - program suffix
On 13/01/11 21:28, Justin A. Lemkul wrote: Instead of installing in the same directory where there are existing executables, what happens if you try to install in a fresh directory? Uhm, I don't get it - how installing in another directory could change their names? I still don't dare to type make install until I see g_hbond_453 instead of g_hbond, for example :) I wanted to make sure you hadn't simply over-written existing executables, or that there was no strange (unexpected) conflict with installing to the same directory. If you're worried about what you're seeing assembled in the source tree vs. what's installed, don't. The binary built in the source tree is g_hbond, but will be installed as g_hbond_453: $ make install ... /bin/sh ../../libtool --mode=install /usr/bin/install -c g_hbond '/home/justin/gmx453/bin/./g_hbond_453' /usr/bin/install -c g_hbond /home/justin/gmx453/bin/./g_hbond_453 Thanks, indeed it works -I didn't think it was make install doing the rename. However now I have another doubt. I installed it in another directory, to be sure, and indeed the /lib /share /include directories keep their original names -and this feels bad because of clashes. So, I wonder: let's say I have a directory gromacs_407 and another gromacs_453. Each of them contains their /bin, /lib, /share, /include, /top. Does each gromacs know to look in its own correct directory for FF files, for example? (so that gromacs_407 looks in gromacs_407/top and gromacs_453 looks in gromacs_453/top ?) thanks! m. -- 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] Installing multiple versions of GROMACS together? - program suffix
devicerandom wrote: On 13/01/11 21:28, Justin A. Lemkul wrote: Instead of installing in the same directory where there are existing executables, what happens if you try to install in a fresh directory? Uhm, I don't get it - how installing in another directory could change their names? I still don't dare to type make install until I see g_hbond_453 instead of g_hbond, for example :) I wanted to make sure you hadn't simply over-written existing executables, or that there was no strange (unexpected) conflict with installing to the same directory. If you're worried about what you're seeing assembled in the source tree vs. what's installed, don't. The binary built in the source tree is g_hbond, but will be installed as g_hbond_453: $ make install ... /bin/sh ../../libtool --mode=install /usr/bin/install -c g_hbond '/home/justin/gmx453/bin/./g_hbond_453' /usr/bin/install -c g_hbond /home/justin/gmx453/bin/./g_hbond_453 Thanks, indeed it works -I didn't think it was make install doing the rename. However now I have another doubt. I installed it in another directory, to be sure, and indeed the /lib /share /include directories keep their original names -and this feels bad because of clashes. So, I wonder: let's say I have a directory gromacs_407 and another gromacs_453. Each of them contains their /bin, /lib, /share, /include, /top. Does each gromacs know to look in its own correct directory for FF files, for example? (so that gromacs_407 looks in gromacs_407/top and gromacs_453 looks in gromacs_453/top ?) Yes. I have several installations dating back to 3.3.3 and have never had a problem. -Justin thanks! m. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Installing multiple versions of GROMACS together? - program suffix
On 14/01/2011 8:48 AM, devicerandom wrote: On 13/01/11 21:28, Justin A. Lemkul wrote: Instead of installing in the same directory where there are existing executables, what happens if you try to install in a fresh directory? Uhm, I don't get it - how installing in another directory could change their names? I still don't dare to type make install until I see g_hbond_453 instead of g_hbond, for example :) I wanted to make sure you hadn't simply over-written existing executables, or that there was no strange (unexpected) conflict with installing to the same directory. If you're worried about what you're seeing assembled in the source tree vs. what's installed, don't. The binary built in the source tree is g_hbond, but will be installed as g_hbond_453: $ make install ... /bin/sh ../../libtool --mode=install /usr/bin/install -c g_hbond '/home/justin/gmx453/bin/./g_hbond_453' /usr/bin/install -c g_hbond /home/justin/gmx453/bin/./g_hbond_453 Thanks, indeed it works -I didn't think it was make install doing the rename. However now I have another doubt. I installed it in another directory, to be sure, and indeed the /lib /share /include directories keep their original names -and this feels bad because of clashes. So, I wonder: let's say I have a directory gromacs_407 and another gromacs_453. Each of them contains their /bin, /lib, /share, /include, /top. Does each gromacs know to look in its own correct directory for FF files, for example? (so that gromacs_407 looks in gromacs_407/top and gromacs_453 looks in gromacs_453/top ?) This is the point of using the GMXRC environment variable. It controls which $GMXDIR/share/top is used by the current invocation of (say) pdb2gmx. If none is specified, then it falls back to the one located in the place it was installed, IIRC. Mark -- 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] extending the simulation with modified mdp option
thanks for your reply. Still i have the same problem. My aim is to extend my simulation from 6ns to 7ns. First i prepared the tpr as grompp_mpi -f nve.mdp -c nve6-g.tpr -o nve7-g.tpr -n crom.ndx where 'nve6-g.tpr' is my old 'tpr' . In the 'nve.mdp' file i have changed the option of storing the 'nstxout' from 1 to 100. That is the only change i have done. For simulation i do, mpirun -nolocal -np 8 -machinefile machine mdrun_mpi -nice 0 -v -s nve7-g.tpr -o nve-g.trr -c nve-g.gro -e nve-g.edr -cpi nve6-g.cpt -g md-g.log -append -cpo nve7-g.cpt -pd From the gromacs website, http://www.gromacs.org/Documentation/How-tos/Extending_Simulations i understood that i need to use the option of 'tpbconv' also to extend the simulation. It says that 'If your old.cpt is for a run that has finished, then use tpbconv -extend after grompp http://www.gromacs.org/grompp and before mdrunhttp://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun.' My 'mdp' options are: title = production-dynamics ;warnings = 10 cpp = /lib/cpp ;DEFINE = -DPOSRES DEFINE = -DFLEXIBLE constraints = none ;constraint_algorithm = shake integrator = md dt = 0.0005 ; nsteps = 200 ; ;nstcomm = 1 ; reset c.o.m motion nstlist= 10 ns_type= grid nstenergy = 1 ; print energies nstlog = 1 ; print to logfile nstvout= 0 ; write velocities nstxout= 100 ; collect data in fs (write coords) ;nstxtcout = 0 ; to print corrdinates to xtc trajectory energygrps = Protein CROM HOH1 HOH2 SOL nstfout= 0 coulombtype= shift fourierspacing = 0.12 pme_order = 4 vdwtype= switch rvdw = 1.0 rvdw_switch= 0.9 rlist = 1.2 rcoulomb = 1.0 rcoulomb-switch= 0.9 pbc= xyz ;dispcorr = Ener continuation = yes ;Berendsen temperature coupling is on Tcoupl = no ; temperature bath (yes, no) ;tau_t = 0.1 ;tc-grps = system ;ref_t = 300 ;Berendsen Pressure coupling is on pcoupl = no ; pressure bath (yes, no) ;pcoupltype = isotropic ;tau_p = 0.5 ;compressibility = 4.5e-05 ;ref_p = 1.0 ;Generate velocities is on at 300 gen_vel = no ; generate initial velocities ;gen_temp= 300.0 ; initial temperature ;gen_seed= 173529; random seeD Please help. thank you, Rama On Wed, Jan 12, 2011 at 3:06 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ramachandran G wrote: Hi gmx-users, I tried extending one of simulation with modified mdp option. First i used the command, grompp -f new.mdp -c old.tpr -o new.tpr then i used the command to extend tpbconv -s new.tpr -extend timetoextendby -o next.tpr Then, mdrun -s next.tpr -cpi previous.cpt I surprised to see the following simulation output, WARNING: This run will generate roughly 2059394074917430016 Mb of data starting mdrun 'GROningen MAchine for Chemical Simulation in water' 200 steps, infinite ps (continuing from step 1200, 6000.0 ps). step 1200 performance: 0.3 ns/daystep 12000100 performance: 0.8 ns/daystep 12000200 performance: 0.8 ns/daystep 12000300 performance: 0.8 ns/day step 12000400 performance: 0.8 ns/daystep 12000500 performance: 0.8 ns/daystep 12000600 performance: 0.8 ns/daystep 12000700 performance: 0.8 ns/daystep 12000800 performance: 0.8 ns/day step 12000900 performance: 0.8 ns/daystep 12001000 performance: 0.8 ns/daystep 12001100 performance: 0.8 ns/day -- Is this correct? Why it needs to generate that much huge Mb of data? I have extended for 1000.0ps but it shows 'infinite ps'. can anybody help me if there is error made in my procedure? It seems like you're trying to extend your run using both grompp and tpbconv, which is not correct. Use one or the other. If you want a real answer to this question, please post real commands, not just the generic format of what should be correct. Also possibly useful is the contents of the .mdp file you used. -Justin Thank you Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] extending the simulation with modified mdp option
On 14/01/2011 10:27 AM, Ramachandran G wrote: thanks for your reply. Still i have the same problem. My aim is to extend my simulation from 6ns to 7ns. First i prepared the tpr as grompp_mpi -f nve.mdp -c nve6-g.tpr -o nve7-g.tpr -n crom.ndx where 'nve6-g.tpr' is my old 'tpr' . In the 'nve.mdp' file i have changed the option of storing the 'nstxout' from 1 to 100. That is the only change i have done. That should be sufficient. You can also try the wiki's suggestion of grompp -t old.cpt. For simulation i do, mpirun -nolocal -np 8 -machinefile machine mdrun_mpi -nice 0 -v -s nve7-g.tpr -o nve-g.trr -c nve-g.gro -e nve-g.edr -cpi nve6-g.cpt -g md-g.log -append -cpo nve7-g.cpt -pd From the gromacs website, http://www.gromacs.org/Documentation/How-tos/Extending_Simulations i understood that i need to use the option of 'tpbconv' also to extend the simulation. It says that 'If your |old.cpt| is for a run that has finished, then use |tpbconv -extend |after grompp http://www.gromacs.org/grompp and before mdrun http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun.' I'd disagree with that last quoted statement, and have updated the wiki accordingly. You need to tell us what GROMACS version you're using. There has been at least one bug fixed in this area in my recent memory, so you may do better with version 4.5.3. Mark My 'mdp' options are: title = production-dynamics ;warnings = 10 cpp = /lib/cpp ;DEFINE = -DPOSRES DEFINE = -DFLEXIBLE constraints = none ;constraint_algorithm = shake integrator = md dt = 0.0005 ; nsteps = 200 ; ;nstcomm = 1 ; reset c.o.m motion nstlist= 10 ns_type= grid nstenergy = 1 ; print energies nstlog = 1 ; print to logfile nstvout= 0 ; write velocities nstxout= 100 ; collect data in fs (write coords) ;nstxtcout = 0 ; to print corrdinates to xtc trajectory energygrps = Protein CROM HOH1 HOH2 SOL nstfout= 0 coulombtype= shift fourierspacing = 0.12 pme_order = 4 vdwtype= switch rvdw = 1.0 rvdw_switch= 0.9 rlist = 1.2 rcoulomb = 1.0 rcoulomb-switch= 0.9 pbc= xyz ;dispcorr = Ener continuation = yes ;Berendsen temperature coupling is on Tcoupl = no ; temperature bath (yes, no) ;tau_t = 0.1 ;tc-grps = system ;ref_t = 300 ;Berendsen Pressure coupling is on pcoupl = no ; pressure bath (yes, no) ;pcoupltype = isotropic ;tau_p = 0.5 ;compressibility = 4.5e-05 ;ref_p = 1.0 ;Generate velocities is on at 300 gen_vel = no ; generate initial velocities ;gen_temp= 300.0 ; initial temperature ;gen_seed= 173529; random seeD Please help. thank you, Rama On Wed, Jan 12, 2011 at 3:06 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ramachandran G wrote: Hi gmx-users, I tried extending one of simulation with modified mdp option. First i used the command, grompp -f new.mdp -c old.tpr -o new.tpr then i used the command to extend tpbconv -s new.tpr -extend timetoextendby -o next.tpr Then, mdrun -s next.tpr -cpi previous.cpt I surprised to see the following simulation output, WARNING: This run will generate roughly 2059394074917430016 Mb of data starting mdrun 'GROningen MAchine for Chemical Simulation in water' 200 steps, infinite ps (continuing from step 1200, 6000.0 ps). step 1200 performance: 0.3 ns/daystep 12000100 performance: 0.8 ns/daystep 12000200 performance: 0.8 ns/daystep 12000300 performance: 0.8 ns/day step 12000400 performance: 0.8 ns/daystep 12000500 performance: 0.8 ns/daystep 12000600 performance: 0.8 ns/daystep 12000700 performance: 0.8 ns/daystep 12000800 performance: 0.8 ns/day step 12000900 performance: 0.8 ns/daystep 12001000 performance: 0.8 ns/daystep 12001100 performance: 0.8 ns/day-- Is this correct? Why it needs to generate that much huge Mb of data? I have extended for 1000.0ps but it shows 'infinite ps'. can anybody help me if there is error made in my procedure? It seems like you're trying to extend your run using both grompp and tpbconv, which is not correct. Use one or the other. If you want a real answer to this question, please post real commands, not just the generic format of what should be correct. Also possibly useful is the contents of the .mdp file you used.
Re: [gmx-users] extending the simulation with modified mdp option
Ramachandran G wrote: thanks for your reply. Still i have the same problem. My aim is to extend my simulation from 6ns to 7ns. First i prepared the tpr as grompp_mpi -f nve.mdp -c nve6-g.tpr -o nve7-g.tpr -n crom.ndx where 'nve6-g.tpr' is my old 'tpr' . In the 'nve.mdp' file i have changed the option of storing the 'nstxout' from 1 to 100. That is the only change i have done. For simulation i do, mpirun -nolocal -np 8 -machinefile machine mdrun_mpi -nice 0 -v -s nve7-g.tpr -o nve-g.trr -c nve-g.gro -e nve-g.edr -cpi nve6-g.cpt -g md-g.log -append -cpo nve7-g.cpt -pd From the gromacs website, http://www.gromacs.org/Documentation/How-tos/Extending_Simulations i understood that i need to use the option of 'tpbconv' also to extend the simulation. It says that 'If your |old.cpt| is for a run that has finished, then use |tpbconv -extend |after grompp http://www.gromacs.org/grompp and before mdrun http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun.' The easiest thing for you to do is to simply extend your run with tpbconv and ignore grompp. If you just need to reduce output volume, post-process the trajectory with trjconv. Otherwise, you have 6 ns of coordinates at every step, then 1 ns of coordinates every 100 steps. The frame interval mismatch will likely cause numerous Gromacs tools to fail, anyway. My 'mdp' options are: title = production-dynamics ;warnings = 10 cpp = /lib/cpp ;DEFINE = -DPOSRES DEFINE = -DFLEXIBLE Flexible water should not be used for MD. http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html constraints = none ;constraint_algorithm = shake integrator = md dt = 0.0005 ; nsteps = 200 ; ;nstcomm = 1 ; reset c.o.m motion nstlist= 10 ns_type= grid nstenergy = 1 ; print energies nstlog = 1 ; print to logfile nstvout= 0 ; write velocities nstxout= 100 ; collect data in fs (write coords) ;nstxtcout = 0 ; to print corrdinates to xtc trajectory energygrps = Protein CROM HOH1 HOH2 SOL nstfout= 0 coulombtype= shift fourierspacing = 0.12 pme_order = 4 vdwtype= switch rvdw = 1.0 rvdw_switch= 0.9 rlist = 1.2 rcoulomb = 1.0 rcoulomb-switch= 0.9 pbc= xyz ;dispcorr = Ener continuation = yes ;Berendsen temperature coupling is on Tcoupl = no ; temperature bath (yes, no) ;tau_t = 0.1 ;tc-grps = system ;ref_t = 300 ;Berendsen Pressure coupling is on pcoupl = no ; pressure bath (yes, no) ;pcoupltype = isotropic ;tau_p = 0.5 ;compressibility = 4.5e-05 ;ref_p = 1.0 ;Generate velocities is on at 300 gen_vel = no ; generate initial velocities ;gen_temp= 300.0 ; initial temperature ;gen_seed= 173529; random seeD You haven't set the tinit parameter in this file. In conjunction with the fact that this .mdp file is for 1 ns, it will start at time zero and run to 1 ns. If you're trying to pick up from the end of a 6-ns simulation, you have two options: 1. Set tinit=6000 and leave nsteps and dt alone. Pass the .cpt file to the -t flag of grompp and run it as if it were a new simulation, then concatenate the output. 2. Set tinit=0 and set nsteps=35 to generate a complete 7-ns .tpr file. Pass this to mdrun in conjunction with your .cpt file from the end of your 6-ns run. 3. Use tpbconv and ignore grompp entirely, then post-process appropriately. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4 -Justin Please help. thank you, Rama On Wed, Jan 12, 2011 at 3:06 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ramachandran G wrote: Hi gmx-users, I tried extending one of simulation with modified mdp option. First i used the command, grompp -f new.mdp -c old.tpr -o new.tpr then i used the command to extend tpbconv -s new.tpr -extend timetoextendby -o next.tpr Then, mdrun -s next.tpr -cpi previous.cpt I surprised to see the following simulation output, WARNING: This run will generate roughly 2059394074917430016 Mb of data starting mdrun 'GROningen MAchine for Chemical Simulation in water' 200 steps, infinite ps (continuing from step 1200, 6000.0 ps). step 1200 performance: 0.3 ns/daystep 12000100 performance: 0.8 ns/daystep 12000200 performance: 0.8 ns/day step 12000300 performance: 0.8 ns/day step 12000400 performance: 0.8 ns/daystep 12000500 performance: 0.8 ns/daystep 12000600 performance: 0.8 ns/day
Re: [gmx-users] extending the simulation with modified mdp option
Hi Mark, Justin, Thanks for your help. The details are helpful to improve my MD simulation. Also i need update my gromacs version from 4.5.1 to 4.5.3. Thanks again, Rama On Thu, Jan 13, 2011 at 3:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ramachandran G wrote: thanks for your reply. Still i have the same problem. My aim is to extend my simulation from 6ns to 7ns. First i prepared the tpr as grompp_mpi -f nve.mdp -c nve6-g.tpr -o nve7-g.tpr -n crom.ndx where 'nve6-g.tpr' is my old 'tpr' . In the 'nve.mdp' file i have changed the option of storing the 'nstxout' from 1 to 100. That is the only change i have done. For simulation i do, mpirun -nolocal -np 8 -machinefile machine mdrun_mpi -nice 0 -v -s nve7-g.tpr -o nve-g.trr -c nve-g.gro -e nve-g.edr -cpi nve6-g.cpt -g md-g.log -append -cpo nve7-g.cpt -pd From the gromacs website, http://www.gromacs.org/Documentation/How-tos/Extending_Simulations i understood that i need to use the option of 'tpbconv' also to extend the simulation. It says that 'If your |old.cpt| is for a run that has finished, then use |tpbconv -extend |after grompp http://www.gromacs.org/grompp and before mdrun http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun.' The easiest thing for you to do is to simply extend your run with tpbconv and ignore grompp. If you just need to reduce output volume, post-process the trajectory with trjconv. Otherwise, you have 6 ns of coordinates at every step, then 1 ns of coordinates every 100 steps. The frame interval mismatch will likely cause numerous Gromacs tools to fail, anyway. My 'mdp' options are: title = production-dynamics ;warnings = 10 cpp = /lib/cpp ;DEFINE = -DPOSRES DEFINE = -DFLEXIBLE Flexible water should not be used for MD. http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html constraints = none ;constraint_algorithm = shake integrator = md dt = 0.0005 ; nsteps = 200 ; ;nstcomm = 1 ; reset c.o.m motion nstlist= 10 ns_type= grid nstenergy = 1 ; print energies nstlog = 1 ; print to logfile nstvout= 0 ; write velocities nstxout= 100 ; collect data in fs (write coords) ;nstxtcout = 0 ; to print corrdinates to xtc trajectory energygrps = Protein CROM HOH1 HOH2 SOL nstfout= 0 coulombtype= shift fourierspacing = 0.12 pme_order = 4 vdwtype= switch rvdw = 1.0 rvdw_switch= 0.9 rlist = 1.2 rcoulomb = 1.0 rcoulomb-switch= 0.9 pbc= xyz ;dispcorr = Ener continuation = yes ;Berendsen temperature coupling is on Tcoupl = no ; temperature bath (yes, no) ;tau_t = 0.1 ;tc-grps = system ;ref_t = 300 ;Berendsen Pressure coupling is on pcoupl = no ; pressure bath (yes, no) ;pcoupltype = isotropic ;tau_p = 0.5 ;compressibility = 4.5e-05 ;ref_p = 1.0 ;Generate velocities is on at 300 gen_vel = no ; generate initial velocities ;gen_temp= 300.0 ; initial temperature ;gen_seed= 173529; random seeD You haven't set the tinit parameter in this file. In conjunction with the fact that this .mdp file is for 1 ns, it will start at time zero and run to 1 ns. If you're trying to pick up from the end of a 6-ns simulation, you have two options: 1. Set tinit=6000 and leave nsteps and dt alone. Pass the .cpt file to the -t flag of grompp and run it as if it were a new simulation, then concatenate the output. 2. Set tinit=0 and set nsteps=35 to generate a complete 7-ns .tpr file. Pass this to mdrun in conjunction with your .cpt file from the end of your 6-ns run. 3. Use tpbconv and ignore grompp entirely, then post-process appropriately. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4 -Justin Please help. thank you, Rama On Wed, Jan 12, 2011 at 3:06 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Ramachandran G wrote: Hi gmx-users, I tried extending one of simulation with modified mdp option. First i used the command, grompp -f new.mdp -c old.tpr -o new.tpr then i used the command to extend tpbconv -s new.tpr -extend timetoextendby -o next.tpr Then, mdrun -s next.tpr -cpi previous.cpt I surprised to see the following simulation output, WARNING: This run will generate roughly 2059394074917430016 Mb of data starting mdrun 'GROningen MAchine for Chemical Simulation in water' 200 steps, infinite ps (continuing from step 1200, 6000.0 ps). step 1200
[gmx-users] Error when execute g_energy - the message: not recognized, maybe different CPU?
Hi, I have an error when try to execute the g_energy program. I'm using Gromacs 4.5.3 version. My Operation System is Ubuntu 9.10. Firstly, my apology if my question is basic, but I'm a computer scientist trying to understand the Gromacs concepts for simulation. My error message appears when I execute the command line: echo '-e' '10' | /usr/local/bin/./g_energy -f /home/faccioli/Execute/EESC_AE/1BDD/energy.edr -o /home/faccioli/Execute/EESC_AE/1BDD/energy.xvg --- Program g_energy, VERSION 4.5.3 Source code file: /home/faccioli/gromacs-4.5.3/src/gmxlib/enxio.c, line: 772 Fatal error: Energy file /home/faccioli/Execute/EESC_AE/1BDD/energy.edr not recognized, maybe different CPU? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- In [1] contains all files which I used in my simulation including the energy file (energy.edr) and all commands which I ran (_run_gromacs.txt). The error message appears when try to execute the 2.pdb file. The others (0.pdb and 1.pdb ) I can get the energy value. These pdb files were build using my implementation of Nerf algorithm [2] which converts dihedral angles to Cartesian coordinates. I looked at line 772 of gmxlib/enxio.c file. However, I didn't understand to fix my problem. I understood my file is not empty, but it is corrupted. So, I couldn't understand how can it is corrupted. [1] http://dl.dropbox.com/u/4270818/compute_energy.zip [2] http://www.ncbi.nlm.nih.gov/pubmed/15898109 I thanks any help. -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 -- 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] Error when execute g_energy - the message: not recognized, maybe different CPU?
Rodrigo Faccioli wrote: Hi, I have an error when try to execute the g_energy program. I'm using Gromacs 4.5.3 version. My Operation System is Ubuntu 9.10. Firstly, my apology if my question is basic, but I'm a computer scientist trying to understand the Gromacs concepts for simulation. My error message appears when I execute the command line: echo '-e' '10' | /usr/local/bin/./g_energy -f /home/faccioli/Execute/EESC_AE/1BDD/energy.edr -o /home/faccioli/Execute/EESC_AE/1BDD/energy.xvg --- Program g_energy, VERSION 4.5.3 Source code file: /home/faccioli/gromacs-4.5.3/src/gmxlib/enxio.c, line: 772 Fatal error: Energy file /home/faccioli/Execute/EESC_AE/1BDD/energy.edr not recognized, maybe different CPU? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- In [1] contains all files which I used in my simulation including the energy file (energy.edr) and all commands which I ran (_run_gromacs.txt). The error message appears when try to execute the 2.pdb file. The others (0.pdb and 1.pdb ) I can get the energy value. These pdb files were build using my implementation of Nerf algorithm [2] which converts dihedral angles to Cartesian coordinates. I looked at line 772 of gmxlib/enxio.c file. However, I didn't understand to fix my problem. I understood my file is not empty, but it is corrupted. So, I couldn't understand how can it is corrupted. [1] http://dl.dropbox.com/u/4270818/compute_energy.zip [2] http://www.ncbi.nlm.nih.gov/pubmed/15898109 I thanks any help. It looks like your EM completely failed. When I ran your input files, I got: Steepest Descents did not converge to Fmax 10 in 2 steps. Potential Energy = 9.9635511e+10 Maximum force = 1.7959855e+13 on atom 122 Norm of force = 2.6216859e+12 This would indicate that perhaps the energy file simply isn't being written properly, since the system has basically exploded immediately such that there are no viable frames. -Justin -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Error when execute g_energy - the message: not recognized, maybe different CPU?
On 14/01/2011 12:12 PM, Rodrigo Faccioli wrote: Hi, I have an error when try to execute the g_energy program. I'm using Gromacs 4.5.3 version. My Operation System is Ubuntu 9.10. Firstly, my apology if my question is basic, but I'm a computer scientist trying to understand the Gromacs concepts for simulation. My error message appears when I execute the command line: echo '-e' '10' | /usr/local/bin/./g_energy -f /home/faccioli/Execute/EESC_AE/1BDD/energy.edr -o /home/faccioli/Execute/EESC_AE/1BDD/energy.xvg --- Program g_energy, VERSION 4.5.3 Source code file: /home/faccioli/gromacs-4.5.3/src/gmxlib/enxio.c, line: 772 Fatal error: Energy file /home/faccioli/Execute/EESC_AE/1BDD/energy.edr not recognized, maybe different CPU? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- Does the .edr file have non-zero size? What does gmxcheck have to say about it? Does the output of gmxdump show that it has plausible data? Mark In [1] contains all files which I used in my simulation including the energy file (energy.edr) and all commands which I ran (_run_gromacs.txt). The error message appears when try to execute the 2.pdb file. The others (0.pdb and 1.pdb ) I can get the energy value. These pdb files were build using my implementation of Nerf algorithm [2] which converts dihedral angles to Cartesian coordinates. I looked at line 772 of gmxlib/enxio.c file. However, I didn't understand to fix my problem. I understood my file is not empty, but it is corrupted. So, I couldn't understand how can it is corrupted. [1] http://dl.dropbox.com/u/4270818/compute_energy.zip [2] http://www.ncbi.nlm.nih.gov/pubmed/15898109 I thanks any help. -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 -- 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] number of cores with a large prime factor
Dear users: I received this error message that gromacs 4.5.3 does not allow me to run on 34 cores. I suggest that this gets put in as a warning (so that I can avoid it if I choose and actually run on 34 cores). A run on 32 cores -npme -1 choose to use 24 particle-particle nodes and 8 PME nodes. I therefore selected 34 cores and -nmpe 10. I don't see how the large prime factor is relevant when -nmpme is not equal to zero. The error message was: Fatal error: The number of nodes you selected (34) contains a large prime factor 17. In most cases this will lead to bad performance. Choose a number with smaller prime factors or set the decomposition (option -dd) manually. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Thoughts? -- 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] Error when execute g_energy - the message: not recognized, maybe different CPU?
Thanks for Justin and Mark their answers. I ran gmxcheck and gmxdump which returned the same error message. Below I show my command lines and the each error message. I would like to know if what I'm doing is the better way to obtain the potential energy of system (protein). I'm asking it because my PhD project is develop an evolutionary algorithm using Gromacs to compute the energy of system. Thanks any help. Below there are the execution of gmxcheck and gmxdump programs when they read my energy file: 1) gmxdump -e energy.edr --- Program gmxdump, VERSION 4.5.3 Source code file: /home/faccioli/gromacs-4.5.3/src/gmxlib/enxio.c, line: 772 Fatal error: Energy file energy.edr not recognized, maybe different CPU? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- 2) gmxcheck -e energy.edr --- Program gmxcheck, VERSION 4.5.3 Source code file: /home/faccioli/gromacs-4.5.3/src/gmxlib/enxio.c, line: 772 Fatal error: Energy file energy.edr not recognized, maybe different CPU? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 On Fri, Jan 14, 2011 at 12:05 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 14/01/2011 12:12 PM, Rodrigo Faccioli wrote: Hi, I have an error when try to execute the g_energy program. I'm using Gromacs 4.5.3 version. My Operation System is Ubuntu 9.10. Firstly, my apology if my question is basic, but I'm a computer scientist trying to understand the Gromacs concepts for simulation. My error message appears when I execute the command line: echo '-e' '10' | /usr/local/bin/./g_energy -f /home/faccioli/Execute/EESC_AE/1BDD/energy.edr -o /home/faccioli/Execute/EESC_AE/1BDD/energy.xvg --- Program g_energy, VERSION 4.5.3 Source code file: /home/faccioli/gromacs-4.5.3/src/gmxlib/enxio.c, line: 772 Fatal error: Energy file /home/faccioli/Execute/EESC_AE/1BDD/energy.edr not recognized, maybe different CPU? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- Does the .edr file have non-zero size? What does gmxcheck have to say about it? Does the output of gmxdump show that it has plausible data? Mark In [1] contains all files which I used in my simulation including the energy file (energy.edr) and all commands which I ran (_run_gromacs.txt). The error message appears when try to execute the 2.pdb file. The others (0.pdb and 1.pdb ) I can get the energy value. These pdb files were build using my implementation of Nerf algorithm [2] which converts dihedral angles to Cartesian coordinates. I looked at line 772 of gmxlib/enxio.c file. However, I didn't understand to fix my problem. I understood my file is not empty, but it is corrupted. So, I couldn't understand how can it is corrupted. [1] http://dl.dropbox.com/u/4270818/compute_energy.zip [2] http://www.ncbi.nlm.nih.gov/pubmed/15898109 I thanks any help. -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 -- 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
Re: [gmx-users] Error when execute g_energy - the message: not recognized, maybe different CPU?
Rodrigo Faccioli wrote: Thanks for Justin and Mark their answers. I ran gmxcheck and gmxdump which returned the same error message. Below I show my command lines and the each error message. I would like to know if what I'm doing is the better way to obtain the potential energy of system (protein). I'm asking it because my PhD project is develop an evolutionary algorithm using Gromacs to compute the energy of system. If you're after a single-point energy, then a zero-step MD is better than a one-step EM, which will, by its nature, try to change your coordinates. The reason (I think) for all the present difficulties is because your coordinates are unreasonable. Have you looked at 2.pdb in, i.e. VMD? The coordinates make no sense, with atoms overlapping each other everywhere. It is for this reason that mdrun basically fails and writes a bad .edr file. -Justin Thanks any help. Below there are the execution of gmxcheck and gmxdump programs when they read my energy file: 1) gmxdump -e energy.edr --- Program gmxdump, VERSION 4.5.3 Source code file: /home/faccioli/gromacs-4.5.3/src/gmxlib/enxio.c, line: 772 Fatal error: Energy file energy.edr not recognized, maybe different CPU? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- 2) gmxcheck -e energy.edr --- Program gmxcheck, VERSION 4.5.3 Source code file: /home/faccioli/gromacs-4.5.3/src/gmxlib/enxio.c, line: 772 Fatal error: Energy file energy.edr not recognized, maybe different CPU? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 On Fri, Jan 14, 2011 at 12:05 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 14/01/2011 12:12 PM, Rodrigo Faccioli wrote: Hi, I have an error when try to execute the g_energy program. I'm using Gromacs 4.5.3 version. My Operation System is Ubuntu 9.10. Firstly, my apology if my question is basic, but I'm a computer scientist trying to understand the Gromacs concepts for simulation. My error message appears when I execute the command line: echo '-e' '10' | /usr/local/bin/./g_energy -f /home/faccioli/Execute/EESC_AE/1BDD/energy.edr -o /home/faccioli/Execute/EESC_AE/1BDD/energy.xvg --- Program g_energy, VERSION 4.5.3 Source code file: /home/faccioli/gromacs-4.5.3/src/gmxlib/enxio.c, line: 772 Fatal error: Energy file /home/faccioli/Execute/EESC_AE/1BDD/energy.edr not recognized, maybe different CPU? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- Does the .edr file have non-zero size? What does gmxcheck have to say about it? Does the output of gmxdump show that it has plausible data? Mark In [1] contains all files which I used in my simulation including the energy file (energy.edr) and all commands which I ran (_run_gromacs.txt). The error message appears when try to execute the 2.pdb file. The others (0.pdb and 1.pdb ) I can get the energy value. These pdb files were build using my implementation of Nerf algorithm [2] which converts dihedral angles to Cartesian coordinates. I looked at line 772 of gmxlib/enxio.c file. However, I didn't understand to fix my problem. I understood my file is not empty, but it is corrupted. So, I couldn't understand how can it is corrupted. [1] http://dl.dropbox.com/u/4270818/compute_energy.zip [2] http://www.ncbi.nlm.nih.gov/pubmed/15898109 I thanks any help. -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes -
[gmx-users] Re: pdb2gmx: segmentation fault
Hi all, I've uploaded my pdb file at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Maybe someone can help me to look into it and see does it has any error. Thanks, Joyce From: Kwee Hong jestan1...@yahoo.com To: gmx-users gmx-users@gromacs.org Sent: Thursday, January 13, 2011 12:21:55 Subject: pdb2gmx: segmentation fault Hi, I was trying to generate topology file of my pdb using pdb2gmx. Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges 4 Opening library file /usr/share/gromacs/top/ffG53a6.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading complex_SurA.pdb... Read 3163 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 409 residues with 3163 atoms chain #res #atoms 1 'B' 409 3163 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/share/gromacs/top/ffG53a6.atp Atomtype 1 Reading residue database... (ffG53a6) Opening library file /usr/share/gromacs/top/ffG53a6.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening library file /usr/share/gromacs/top/ffG53a6.hdb Opening library file /usr/share/gromacs/top/ffG53a6-n.tdb Opening library file /usr/share/gromacs/top/ffG53a6-c.tdb Back Off! I just backed up topol_SurA.top to ./#topol_SurA.top.1# Processing chain 1 'B' (3163 atoms, 409 residues) There are 629 donors and 614 acceptors Segmentation fault Yet I encountered segmentation fault which I don't understand why this happen. All suggestion are welcomed? Thanks. Joyce -- 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] number of cores with a large prime factor
On 01/14/11, chris.ne...@utoronto.ca wrote: Dear users: I received this error message that gromacs 4.5.3 does not allow me to run on 34 cores. I suggest that this gets put in as a warning (so that I can avoid it if I choose and actually run on 34 cores). A run on 32 cores -npme -1 choose to use 24 particle-particle nodes and 8 PME nodes. I therefore selected 34 cores and -nmpe 10. I don't see how the large prime factor is relevant when -nmpme is not equal to zero. The MPMD communication load is much smaller if there's a large common factor in the largest element of both the DD grid and the PME grid. With 24 and 10, the best common factor is 2, and the combination of 4x3x2 (or 8x3x1) and 2x5x1 grids would be poor. I bet that if you could run this job, it would be markedly slower than the 32-core one above. The architecture of the communication hardware is important here, and you do want any intrinsic values (like cores per Infiniband connection) to be a factor of that large common factor. This can have a very large effect on performance - I have a publication due out shortly that demonstrates that on 64 processors of BlueGene/L, npme=0 and npme=32 run faster than any other value (with other parameters optimized so as to produce equivalent error in the PME approximation), and this is because of the communication topology. The error message was: Fatal error: The number of nodes you selected (34) contains a large prime factor 17. In most cases this will lead to bad performance. Choose a number with smaller prime factors or set the decomposition (option -dd) manually. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Thoughts? This change arose from this discussion http://redmine.gromacs.org/issues/551. As you can see from the timing numbers I report there, one really does not want large prime factors in either N_pme or N_pp, and thus in the number of nodes (because you want a large non-prime common factor). The GROMACS defaults achieve decent results if you request multiples that reflect your hardware reality, and avoid comparably large prime factors. Mark -- 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] Re: pdb2gmx: segmentation fault
On 01/14/11, Kwee Hong jestan1...@yahoo.com wrote:
!-- DIV {margin:0px;} --
Hi all,
I've uploaded my pdb file
at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb
Maybe someone can help me to look into it and see does it has any error.
That link does not work.
Mark
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Re: [gmx-users] Re: pdb2gmx: segmentation fault
Sorry, this should be correct link to download the file. http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb Joyce From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, January 14, 2011 11:29:45 Subject: Re: [gmx-users] Re: pdb2gmx: segmentation fault On 01/14/11, Kwee Hong jestan1...@yahoo.com wrote: Hi all, I've uploaded my pdb file at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Maybe someone can help me to look into it and see does it has any error. That link does not work. Mark -- 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] Re: pdb2gmx: segmentation fault
Kwee Hong wrote: Sorry, this should be correct link to download the file. http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb This link also does not work. -Justin http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Joyce *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, January 14, 2011 11:29:45 *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault On 01/14/11, *Kwee Hong * jestan1...@yahoo.com wrote: Hi all, I've uploaded my pdb file at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Maybe someone can help me to look into it and see does it has any error. That link does not work. Mark -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Re: pdb2gmx: segmentation fault
Sorry. Sorry. This would be the working one. I've tested it outside my uni domain. http://www.birg1.fbb.utm.my/joyce/protein_dock.pdb joyce From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, January 14, 2011 11:57:01 Subject: Re: [gmx-users] Re: pdb2gmx: segmentation fault Kwee Hong wrote: Sorry, this should be correct link to download the file. http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb This link also does not work. -Justin http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Joyce *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, January 14, 2011 11:29:45 *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault On 01/14/11, *Kwee Hong * jestan1...@yahoo.com wrote: Hi all, I've uploaded my pdb file at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Maybe someone can help me to look into it and see does it has any error. That link does not work. Mark -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Re: pdb2gmx: segmentation fault
Kwee Hong wrote: Sorry. Sorry. This would be the working one. I've tested it outside my uni domain. http://www.birg1.fbb.utm.my/joyce/protein_dock.pdb Remove the www and it works for me. Your .pdb file has several problems: 1. Loads of blank space at the end. 2. All lines are misformatted, with all columns after the chain identifier shifted by one space. In vi, use :1,$s/ B / B/g to fix it. This alleviates the seg fault. 3. Asn106 has its N atom labeled as residue 105. Fixing all of the above resulted in a usable topology with Gromacs 4.5.3. -Justin http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb joyce *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, January 14, 2011 11:57:01 *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault Kwee Hong wrote: Sorry, this should be correct link to download the file. http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb This link also does not work. -Justin http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Joyce *From:* Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Friday, January 14, 2011 11:29:45 *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault On 01/14/11, *Kwee Hong * jestan1...@yahoo.com mailto:jestan1...@yahoo.com wrote: Hi all, I've uploaded my pdb file at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Maybe someone can help me to look into it and see does it has any error. That link does not work. Mark -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Re: pdb2gmx: segmentation fault
On 01/14/11, Kwee Hong jestan1...@yahoo.com wrote:
!-- DIV {margin:0px;} --
Sorry. Sorry.
This would be the working one. I've tested it outside my uni domain.
http://www.birg1.fbb.utm.my/joyce/protein_dock.pdb(http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb)
Still dead.
Mark
joyce
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Friday, January 14, 2011 11:57:01
Subject: Re: [gmx-users] Re: pdb2gmx: segmentation fault
Kwee Hong wrote:
Sorry, this should be correct link to download the file.
http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb
This link also does not work.
-Justin
http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb
Joyce
*From:* Mark Abraham mark.abra...@anu.edu.au
*To:* Discussion list
for GROMACS users gmx-users@gromacs.org
*Sent:* Friday, January 14, 2011 11:29:45
*Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault
On 01/14/11, *Kwee Hong * jestan1...@yahoo.com wrote:
Hi all,
I've uploaded my pdb file
at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb
Maybe someone can help me to look into it and see does it has any error.
That link does not work.
Mark
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS
Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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Re: [gmx-users] Re: pdb2gmx: segmentation fault
It works. Thanks a lot From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Friday, January 14, 2011 12:18:45 Subject: Re: [gmx-users] Re: pdb2gmx: segmentation fault Kwee Hong wrote: Sorry. Sorry. This would be the working one. I've tested it outside my uni domain. http://www.birg1.fbb.utm.my/joyce/protein_dock.pdb Remove the www and it works for me. Your .pdb file has several problems: 1. Loads of blank space at the end. 2. All lines are misformatted, with all columns after the chain identifier shifted by one space. In vi, use :1,$s/ B / B/g to fix it. This alleviates the seg fault. 3. Asn106 has its N atom labeled as residue 105. Fixing all of the above resulted in a usable topology with Gromacs 4.5.3. -Justin http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb joyce *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, January 14, 2011 11:57:01 *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault Kwee Hong wrote: Sorry, this should be correct link to download the file. http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb This link also does not work. -Justin http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Joyce *From:* Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Friday, January 14, 2011 11:29:45 *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault On 01/14/11, *Kwee Hong * jestan1...@yahoo.com mailto:jestan1...@yahoo.com wrote: Hi all, I've uploaded my pdb file at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Maybe someone can help me to look into it and see does it has any error. That link does not work. Mark -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Re: pdb2gmx: segmentation fault
But Justin got it... From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, January 14, 2011 12:18:49 Subject: Re: [gmx-users] Re: pdb2gmx: segmentation fault On 01/14/11, Kwee Hong jestan1...@yahoo.com wrote: Sorry. Sorry. This would be the working one. I've tested it outside my uni domain. http://www.birg1.fbb.utm.my/joyce/protein_dock.pdb Still dead. Mark joyce From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, January 14, 2011 11:57:01 Subject: Re: [gmx-users] Re: pdb2gmx: segmentation fault Kwee Hong wrote: Sorry, this should be correct link to download the file. http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb This link also does not work. -Justin http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Joyce *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, January 14, 2011 11:29:45 *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault On 01/14/11, *Kwee Hong * jestan1...@yahoo.com wrote: Hi all, I've uploaded my pdb file at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Maybe someone can help me to look into it and see does it has any error. That link does not work. Mark -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Re: pdb2gmx: segmentation fault
Kwee Hong wrote: But Justin got it... Yes, but only after modifying the URL, as I indicated in my last message. -Justin *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, January 14, 2011 12:18:49 *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault On 01/14/11, *Kwee Hong * jestan1...@yahoo.com wrote: Sorry. Sorry. This would be the working one. I've tested it outside my uni domain. http://www.birg1.fbb.utm.my/joyce/protein_dock.pdb http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb Still dead. Mark joyce *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, January 14, 2011 11:57:01 *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault Kwee Hong wrote: Sorry, this should be correct link to download the file. http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb This link also does not work. -Justin http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Joyce *From:* Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Friday, January 14, 2011 11:29:45 *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault On 01/14/11, *Kwee Hong * jestan1...@yahoo.com mailto:jestan1...@yahoo.com wrote: Hi all, I've uploaded my pdb file at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb Maybe someone can help me to look into it and see does it has any error. That link does not work. Mark -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Doubts regarding Simulation box - Thanks
Thank you Tsjerk for your suggestions! So according to this my minimal box size should be 0.6nm in order to avoid PBS effects and due to the water effects i have to set it 1nm or higher. So this rule is irrespective of the box type we choose isnt it? I got the clue for my second question. Thanks a lot! MKS -- 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] Density of the box
Thank you Tsjerk! Actually I was not using any dummy atoms or united atoms in this case. I was using a pdb file with just water atoms (1BP2). Kindly excuse me I was not recieving any replys to my mail id ka...@rishi.serc.iisc.ernet.in. -- 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] Doubts regarding Simulation box - Thanks
Hi MKS, So according to this my minimal box size should be 0.6nm in order to avoid PBS effects and due to the water effects i have to set it 1nm or higher. Well, not box size, but the distance from the solute to the box wall :) So this rule is irrespective of the box type we choose isnt it? Yes. You want to be sure to have at least the minimal distance between images, i.e. two times the distance from the solute to the wall, everywhere. I got the clue for my second question. Good :) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Doubts regarding Simulation box - Thanks
On 01/14/11, Kavyashree M hmkv...@gmail.com wrote: Thank you Tsjerk for your suggestions! Please leave old email context in so that people can find out what you are talking about. Only to you is your email so important that you might remember all the details :-) So according to this my minimal box size should be 0.6nm in order to avoid PBS effects and due to the water effects i have to set it 1nm or higher. So this rule is irrespective of the box type we choose isnt it? 1) You need a minimum amount of water between solutes to have a reasonably physical model. 2) You wish to minimize the cost of that water by the choice of box shape and size. Mark -- 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] TZD Tautomers
Nancy, Mark already indicated that this is not the proper place to post questions like that. This forum is about gromacs, not about tautomers, docking, and certainly not about MarvinSketch. Cheers, Tsjerk On Thu, Jan 13, 2011 at 10:26 PM, Nancy nancy5vi...@gmail.com wrote: Hi All, I happened to find a published article where molecular docking simulations of TZDs against a novel protein is detailed: Structure-based design of a thiazolidinedione which targets the mitochondrial protein mitoNEET Bioorg Med Chem Lett. 2010 Feb 1;20(3):819-23 In this paper, the authors, using MarvinSketch v3.5.4, determined that the TZDs would exist predominantly in the enol form at pH 7.4, as opposed to the diketone form (see attached figure). It appears that the article's tautomer prediction was based only on the pH prior to docking, and had nothing to do with ligand-protein interactions. Does anyone know if the diketone or enol, or perhaps a different tautomer, would be predominant at pH 7.4? Thanks in advance. Nancy -- gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Doubts regarding Simulation box - Thanks
Thanks Tsjerk and Mark! After setting the box I measured the distance of the last protein atom and the box edge it was not same all the sides. Any comments on this? I have sent another question regarding minimization but no replys yet. Kindly reply Sir! Thanking you MKS On Fri, Jan 14, 2011 at 10:42 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 01/14/11, *Kavyashree M * hmkv...@gmail.com wrote: Thank you Tsjerk for your suggestions! Please leave old email context in so that people can find out what you are talking about. Only to you is your email so important that you might remember all the details :-) So according to this my minimal box size should be 0.6nm in order to avoid PBS effects and due to the water effects i have to set it 1nm or higher. So this rule is irrespective of the box type we choose isnt it? 1) You need a minimum amount of water between solutes to have a reasonably physical model. 2) You wish to minimize the cost of that water by the choice of box shape and size. Mark -- 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
