Re: [gmx-users] Fwd: Command line to obtain multiple eigenvectors
On 3/1/13 2:54 AM, Ashalatha Sreshty wrote: Dear Justin, I did the same before but didnot get the eigenvectors. I am working on Gromacs-4.5.4. The actual command line used is as below g_anaeig_d -f mlecdig-MD-0-202-noPBC.xtc -s mlecdig-MD-1.tpr -v eigenvec-mlecdig-2-102.trr -eig eigenval-mlecdig-2-102.xvg -n mlecdig.ndx -proj proj14.xvg -first 1 -last 4 -b 2 -e 102 -tu ns However, I didnot get all the four eigenvectors in the output file, but only consisted of the first eigenvector. Sample lines from the output I pastign it here for your ready reference: 2.2.89116 2.00503.68519 2.01002.44595 2.01501.92587 2.02002.11691 2.02501.26153 2.03000.98976 2.03501.23497 2.04001.27905 2.04502.31289 2.05001.23402 2.05502.09228 2.06002.20607 2.06502.00745 2.07002.32700 2.07501.98665 2.08002.56843 2.08502.51773 2.09002.86463 Please suggest. There should be four data sets written to proj14.xvg, separated by ampersands (). I have verified that this approach should work; please inspect your output file carefully. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Gromos43A1-S3 lipid parameters
Thanks Justin and Kukol for the info. Kukol, Can you please upload the cholesterol parameters also in the site you provided, if you have??. On Fri, Mar 1, 2013 at 2:02 PM, Kukol, Andreas a.ku...@herts.ac.uk wrote: Hello Venkat, You can use Gromos96 53a6 lipid parameters for DPPC, DMPC, POPC and POPG with the Gromos96 53a6 force field. They can be downloaded from here: https://sites.google.com/site/bioherts/home/lipid-topologies Reference: Kukol, A., 2009. Lipid models for united-atom molecular dynamics simulations of proteins. J. Chem. Theor. Comput., 5(3), 615-626. Andreas -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: 28 February 2013 13:51 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Gromos43A1-S3 lipid parameters On 2/28/13 2:16 AM, Venkat Reddy wrote: Dear all, Can I use Gromos43A1-S3 lipid parameters provided in the GROMACS site along with the GROMOS53a6 forcefield in the same manner as Justin has explained in his KALP15 tutorial? It's probably more sensible to use 43A1, since that's the basis for the 43A1-S3 lipids. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] do_dssp
I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/src/tools/gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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] do_dssp with 4.6
Dear gmx users, Has anyone tried dssp-2.1.0 with gromacs-4.6? I am having the common problems that were supossed not to be in the new releases -- 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] do_dssp
With -ver, just like it says. do_dssp -h explains how. What dssp version do you have? Erik On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/src/tools/ gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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] removing number of sol
Dear All, I know the residue numbers of SOL molecules (which are more than thousands) which I want to remove them from a gro file. I searched that make_ndx can be used make a index file to define residues. But It is a prompt based tool and its difficult to type manually thousands of residue numbers. 1) Is there some way to feed the residue numbers to make_ndx? Or I need to make index file format my self by some scritpting Or is there is rather easier way of doing in gromacs. 2) Also is there any direct command which helps to remove a residue number directly from a gro file without using index file input; means residue defined in command itself? 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. 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
[gmx-users] Re:Re: wrong bonds generate by g_x2top
Dear Justin: Thank you for reply. g_x2top worked correct as you suggested when I added -nopbc option. I have other questions about graphite simulation. The top/rtp file(opls-aa) generated by g_x2top missed improper dihedral term , to keep a carbon in plane, whether it is better to add the missing terms in topology file or need other corrections ? Thank you in advance! sincerely zhhxu PhD student Department of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences -- 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] removing number of sol
The ndx format is really simple. You can easily script your way to a new index group as long as the selection of atoms can be automated. Furthermore, the gro format is also simple, so you can filter out the unwanted residues there instead of using an index file. Erik On Mar 1, 2013, at 1:42 PM, gromacs query wrote: Dear All, I know the residue numbers of SOL molecules (which are more than thousands) which I want to remove them from a gro file. I searched that make_ndx can be used make a index file to define residues. But It is a prompt based tool and its difficult to type manually thousands of residue numbers. 1) Is there some way to feed the residue numbers to make_ndx? Or I need to make index file format my self by some scritpting Or is there is rather easier way of doing in gromacs. 2) Also is there any direct command which helps to remove a residue number directly from a gro file without using index file input; means residue defined in command itself? 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. 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 -- 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] do_dssp
What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD) in your terminal? Erik On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/src/tools/ gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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] removing number of sol
Dear Erik, so you can filter out the unwanted residues there instead of using an index file. There are thousands of water to be removed so simple commands like sed exhausts when I run it in loops. e.g. Just to say : sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e '/40SOL/d' -e '/41SOL/d' -e '/42SOL/d' -e '/43SOL/d' -e '/44SOL/d' -e '/45SOL/d' old.gro new2.gro this will remove such 10 residues but if you run this again and again (in text exe format) say 1000 times it exhausts some how and remove waters which are not even mentioned in sed command! I have checked it many times. So I thought if index file could help me. But please reply for point 3: 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . thanks, This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund er...@xray.bmc.uu.se wrote: The ndx format is really simple. You can easily script your way to a new index group as long as the selection of atoms can be automated. Furthermore, the gro format is also simple, so you can filter out the unwanted residues there instead of using an index file. Erik On Mar 1, 2013, at 1:42 PM, gromacs query wrote: Dear All, I know the residue numbers of SOL molecules (which are more than thousands) which I want to remove them from a gro file. I searched that make_ndx can be used make a index file to define residues. But It is a prompt based tool and its difficult to type manually thousands of residue numbers. 1) Is there some way to feed the residue numbers to make_ndx? Or I need to make index file format my self by some scritpting Or is there is rather easier way of doing in gromacs. 2) Also is there any direct command which helps to remove a residue number directly from a gro file without using index file input; means residue defined in command itself? 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] removing number of sol
On 3/1/13 7:58 AM, gromacs query wrote: Dear Erik, so you can filter out the unwanted residues there instead of using an index file. There are thousands of water to be removed so simple commands like sed exhausts when I run it in loops. e.g. Just to say : sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e '/40SOL/d' -e '/41SOL/d' -e '/42SOL/d' -e '/43SOL/d' -e '/44SOL/d' -e '/45SOL/d' old.gro new2.gro this will remove such 10 residues but if you run this again and again (in text exe format) say 1000 times it exhausts some how and remove waters which are not even mentioned in sed command! I have checked it many times. So I thought if index file could help me. But please reply for point 3: 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . I don't know about editconf, but trjconv can do this. -Justin thanks, This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund er...@xray.bmc.uu.se wrote: The ndx format is really simple. You can easily script your way to a new index group as long as the selection of atoms can be automated. Furthermore, the gro format is also simple, so you can filter out the unwanted residues there instead of using an index file. Erik On Mar 1, 2013, at 1:42 PM, gromacs query wrote: Dear All, I know the residue numbers of SOL molecules (which are more than thousands) which I want to remove them from a gro file. I searched that make_ndx can be used make a index file to define residues. But It is a prompt based tool and its difficult to type manually thousands of residue numbers. 1) Is there some way to feed the residue numbers to make_ndx? Or I need to make index file format my self by some scritpting Or is there is rather easier way of doing in gromacs. 2) Also is there any direct command which helps to remove a residue number directly from a gro file without using index file input; means residue defined in command itself? 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist 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:Re: wrong bonds generate by g_x2top
On 3/1/13 7:47 AM, zhhxu wrote: Dear Justin: Thank you for reply. g_x2top worked correct as you suggested when I added -nopbc option. I have other questions about graphite simulation. The top/rtp file(opls-aa) generated by g_x2top missed improper dihedral term , to keep a carbon in plane, whether it is better to add the missing terms in topology file or need other corrections ? If you need to keep groups planar, then you need impropers. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] removing number of sol
On Mar 1, 2013, at 1:58 PM, gromacs query wrote: Dear Erik, so you can filter out the unwanted residues there instead of using an index file. There are thousands of water to be removed so simple commands like sed exhausts when I run it in loops. e.g. Just to say : sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e '/ 40SOL/d' -e '/41SOL/d' -e '/42SOL/d' -e '/43SOL/d' -e '/44SOL/d' -e '/45SOL/d' old.gro new2.gro this will remove such 10 residues but if you run this again and again (in text exe format) say 1000 times it exhausts some how and remove waters which are not even mentioned in sed command! I have checked it many times. So I thought if index file could help me. But please reply for point 3: First of all, that's not a safe way of removing waters. Note that both SOL 35, SOL 135, ... will be removed by that command. Secondly, I'm sure you can think of a better way of scripting it, using e.g. sed or awk. By which criteria do you select the waters to be removed? 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . thanks, This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund er...@xray.bmc.uu.se wrote: The ndx format is really simple. You can easily script your way to a new index group as long as the selection of atoms can be automated. Furthermore, the gro format is also simple, so you can filter out the unwanted residues there instead of using an index file. Erik On Mar 1, 2013, at 1:42 PM, gromacs query wrote: Dear All, I know the residue numbers of SOL molecules (which are more than thousands) which I want to remove them from a gro file. I searched that make_ndx can be used make a index file to define residues. But It is a prompt based tool and its difficult to type manually thousands of residue numbers. 1) Is there some way to feed the residue numbers to make_ndx? Or I need to make index file format my self by some scritpting Or is there is rather easier way of doing in gromacs. 2) Also is there any direct command which helps to remove a residue number directly from a gro file without using index file input; means residue defined in command itself? 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] removing number of sol
On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote: On Mar 1, 2013, at 1:58 PM, gromacs query wrote: Dear Erik, so you can filter out the unwanted residues there instead of using an index file. There are thousands of water to be removed so simple commands like sed exhausts when I run it in loops. e.g. Just to say : sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e '/ 40SOL/d' -e '/41SOL/d' -e '/42SOL/d' -e '/43SOL/d' -e '/44SOL/d' -e '/45SOL/d' old.gro new2.gro this will remove such 10 residues but if you run this again and again (in text exe format) say 1000 times it exhausts some how and remove waters which are not even mentioned in sed command! I have checked it many times. So I thought if index file could help me. But please reply for point 3: First of all, that's not a safe way of removing waters. Note that both SOL 35, SOL 135, ... will be removed by that command. Secondly, I'm sure you can think of a better way of scripting it, using e.g. sed or awk. By which criteria do you select the waters to be removed? If its a contiguous chunk then it's dead simple. 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . thanks, This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund er...@xray.bmc.uu.se wrote: The ndx format is really simple. You can easily script your way to a new index group as long as the selection of atoms can be automated. Furthermore, the gro format is also simple, so you can filter out the unwanted residues there instead of using an index file. Erik On Mar 1, 2013, at 1:42 PM, gromacs query wrote: Dear All, I know the residue numbers of SOL molecules (which are more than thousands) which I want to remove them from a gro file. I searched that make_ndx can be used make a index file to define residues. But It is a prompt based tool and its difficult to type manually thousands of residue numbers. 1) Is there some way to feed the residue numbers to make_ndx? Or I need to make index file format my self by some scritpting Or is there is rather easier way of doing in gromacs. 2) Also is there any direct command which helps to remove a residue number directly from a gro file without using index file input; means residue defined in command itself? 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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 thewww 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
Re: [gmx-users] removing number of sol
Aha! thanks Erik (and Justin), I really feel sorry 35 and 135 will be removed by sed. I must have given a thought about that. So this was reason sed was over doing the things. Also as you asked: They are random residue number water molecules so not continuous and they were selected on the criteria based on X Y Z coordinates (some space fixed and outlier waters are to be removed) regards, On Fri, Mar 1, 2013 at 3:09 PM, Erik Marklund er...@xray.bmc.uu.se wrote: On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote: On Mar 1, 2013, at 1:58 PM, gromacs query wrote: Dear Erik, so you can filter out the unwanted residues there instead of using an index file. There are thousands of water to be removed so simple commands like sed exhausts when I run it in loops. e.g. Just to say : sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e '/40SOL/d' -e '/41SOL/d' -e '/42SOL/d' -e '/43SOL/d' -e '/44SOL/d' -e '/45SOL/d' old.gro new2.gro this will remove such 10 residues but if you run this again and again (in text exe format) say 1000 times it exhausts some how and remove waters which are not even mentioned in sed command! I have checked it many times. So I thought if index file could help me. But please reply for point 3: First of all, that's not a safe way of removing waters. Note that both SOL 35, SOL 135, ... will be removed by that command. Secondly, I'm sure you can think of a better way of scripting it, using e.g. sed or awk. By which criteria do you select the waters to be removed? If its a contiguous chunk then it's dead simple. 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . thanks, This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund er...@xray.bmc.uu.se wrote: The ndx format is really simple. You can easily script your way to a new index group as long as the selection of atoms can be automated. Furthermore, the gro format is also simple, so you can filter out the unwanted residues there instead of using an index file. Erik On Mar 1, 2013, at 1:42 PM, gromacs query wrote: Dear All, I know the residue numbers of SOL molecules (which are more than thousands) which I want to remove them from a gro file. I searched that make_ndx can be used make a index file to define residues. But It is a prompt based tool and its difficult to type manually thousands of residue numbers. 1) Is there some way to feed the residue numbers to make_ndx? Or I need to make index file format my self by some scritpting Or is there is rather easier way of doing in gromacs. 2) Also is there any direct command which helps to remove a residue number directly from a gro file without using index file input; means residue defined in command itself? 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing
Re: [gmx-users] GPU version of GROMACS 4.6 in MacOS cluster
Hi Szilαrd Thanks for your reply. I have run the deviceQuery utility and what I got back is /deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) cudaGetDeviceCount returned 38 - no CUDA-capable device is detected Should I understand from this that the CUDA driver was not installed from the MAC OS X CUDA 5.0 Production Release? George HI, That looks like the driver does not work or is incompatible with the runtime. Please get the SDK, compile a simple program, e.g. deviceQuery and see if that works (I suspect that it won't). Regarding your machines, just FYI, the Quadro 4000 is a pretty slow card (somewhat slower than a GTX 460) so you'll hava a quite strong resource imbalance: a lot of CPU compute power (2x Xeon 5xxx, right?) and little GPU compute power which will lead to the CPU idling while waiting for the GPU. Cheers, -- Szilαrd On Thu, Feb 28, 2013 at 4:52 PM, George Patargias g...@bioacademy.grwrote: Hello We are trying to install the GPU version of GROMACS 4.6 on our own MacOS cluster. So for the cluster nodes that have the NVIDIA Quadro 4000 cards: - We have downloaded and install the MAC OS X CUDA 5.0 Production Release from here: https://developer.nvidia.com/cuda-downloads placing the libraries contained in this download in /usr/local/cuda/lib - We have managed to compile GROMACS 4.6 linking it statically with these CUDA libraries and the MPI libraries (with BUILD_SHARED_LIBS=OFF and GMX_PREFER_STATIC_LIBS=ON) Unfortunately, when we tried to run a test job with the generated mdrun_mpi, GROMACS reported that it cannot detect any CUDA-enabled devices. It also reports 0.0 version for CUDA driver and runtime. Is the actual CUDA driver missing from the MAC OS X CUDA 5.0 Production Release that we installed? Do we need to install it from here: http://www.nvidia.com/object/cuda-mac-driver.html Or is something else that we need to do? Many thanks in advance. George Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- 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 Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- 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
AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current
Hi, Now I've tested the version of g_current in 4.6 and for me it works fine. /Flo -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von Florian Dommert Gesendet: Mittwoch, 27. Februar 2013 18:46 An: 'Discussion list for GROMACS users' Betreff: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von Nilesh Dhumal Gesendet: Mittwoch, 27. Februar 2013 17:38 An: Discussion list for GROMACS users Betreff: Re: AW: AW: AW: AW: AW: AW: [gmx-users] g_current Hello, I am using g_current for first time. Now I am running additional simulation and I will save trajectory at 2 fs. Is it possible to calculate contribution of rotational and translation to dipole moment simultaneously with the simulation instead of saving the trajectory at each 2fs? Hi, This is one of my majors on my to do list, but currently not possible. I think a saving frequency of 0.05 ps should be fine. /Flo Nilesh Hi, Have you done a similar analysis with another IL system or is it the first time you use g_current? Currently I am not able to figure out what the problem is. However 2ps saving interval is quite long for such a kind of analysis. A zero value of the translational dipole moment hints to neutral molecules which should not be the case for your system. What is written in the output of mj.xvg. Is filled with zeros? /Flo -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von Nilesh Dhumal Gesendet: Mittwoch, 27. Februar 2013 15:26 An: Discussion list for GROMACS users Betreff: Re: AW: AW: AW: AW: AW: [gmx-users] g_current Hello, Yes. Segfault is solved. I saving velocites and coordinates at 2 ps. Nilesh Hi, At least the segfault is solved. However, the zero output of M_J for your IL system is really strange. I'm thinking about a reason, but I am currently not able to find one. How often do you write out velocities and coordinates in your trr file? /Flo -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von Nilesh Dhumal Gesendet: Dienstag, 26. Februar 2013 17:50 An: Discussion list for GROMACS users Betreff: Re: AW: AW: AW: AW: [gmx-users] g_current Hello, I didn't get any segmental fault if I use Gromacs Version 4.5.5. g_current -f md.trr -s md.tpr -mc Program didn't write the mc.xvg Average translational dipole moment is zero. Average translational dipole moment M_J [enm] after 15001 frames (|M|^2): -0.00 -0.00 -0.00 (0.00) Can you tell where is the problem? Nilesh Hi, I am using the release branch of 4.5. /Flo --- Florian Dommert Dipl. Phys. Institut für Computerphysik Universität Stuttgart Allmandring 3 D-70569 Stuttgart Tel.: 0711-68563613 Fax: 0711-68563658 -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von Nilesh Dhumal Gesendet: Montag, 25. Februar 2013 15:35 An: Discussion list for GROMACS users Betreff: Re: AW: AW: AW: [gmx-users] g_current Hello, Thanks. I will update Gromacs version. Can you tell which version you are using ? Nilesh Hi, Can you update your Gromacs version to an actual release and check if the problem still occurs. It is very strange that the Einstein-Helfand fit gives 0 for sigma and M_J^2. Cheers, Flo --- Florian Dommert Dipl. Phys. Institut für Computerphysik Universität Stuttgart Allmandring 3 D-70569 Stuttgart Tel.: 0711-68563613 Fax: 0711-68563658 -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] Im Auftrag von Nilesh Dhumal Gesendet: Montag, 25. Februar 2013 14:00 An: Discussion list for GROMACS users Betreff: Re: AW: AW: [gmx-users] g_current Hello, I am using Gromacs VERSION 4.0.7. Nilesh Hi, Which version of gromacs are you using. I am applying this tool also to ILs and it works fine for me in the release-4-5 branch. It is especially strange that you have a rotational dipole moment of zero. However, currently I have no idea where the segfault arises. Especially because you get an output. So
[gmx-users] distance restraint
Hi everyone! I want to add the distance restraint for some atom pairs. However, it is not working at all. The yielded bond length can easily go beyond 0.5~0.6 nm. Has anyone got a hint? Thanks very much! [ distance_restraints] ; ai aj type index type' low up1 up2 fac 15791010.000.400.42100 15771010.000.400.42100 21471110.000.400.42100 21461110.000.400.42100 275 1210.000.400.42100 27451210.000.400.42100 33781310.000.400.42100 33821310.000.400.42100 51114 1410.000.400.42100 51111 1410.000.400.42100 57471510.000.400.42100 57431510.000.400.42100 639 1610.000.400.42100 635 1610.000.400.42100 69117 1710.000.400.42100 Best regards, Linlin Sun -- 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] protein-ligand simulation-query
Dear gromacs users, I am performing united atom simulations of a hydrophobic drug and its ligand with 53a6 ff. Should I instead choose an all atom force field in order to reproduce all the protein-drug interactions for accuracy? Thank you in advance. Regards, Revathi -- 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 bars - g_wham
Hi Stephen, computing errors from umbrella sampling is not trivial at al. Generally, there are two possibilities: - If each histogram overlaps only with one neighboring histogram, you *must* know the autocorrelation time of each window. This is often a problem in MD simulations, because there may be hidden slow transitions. In my experience, you always underestimate the autocorrelation time and as a consequence the statistical error. However, if you do know the autocorrelation time, then you can either (a) compute the PMF from blocks of the data (how you did), but this only works if the blocks are longer than the autocorrelation time or (b) use g_wham -bs-method traj to generate new synthentic histograms for bootstrapping (which incorporate the autocorrelation time). Important: You cannot do bootstrapping of complete histograms, because there is only one histogram at each window. - If you have many histograms overlapping each other, or if you did umbrella sampling at each window multiple times, you can assume that the different histograms represent all possible histograms at the respective position of the reaction coordinate. Then, you can do bootstrapping of histograms with g_wham -bs-method b-hist. It is not obvious how many histograms you need at each position, but maybe 10 is a reasonable number. Coming to your error from blocks of data (10-30, 30-50, 50-70, 70-100 ns). The small error you get could mean two things: a) you have a well-converged PMF (good) b) you have long autocorrelations. Therefore, the histograms from the blocks are similar. Therefore, you underestimate the error (bad). So you see, it is not trivial to estimate errors from umbrella sampling. My experience is that bootstrapping of histograms is more reliable, but it requires that you have multiple histograms at each position (and these histograms should be uncorrelated!!). But at least, this way you do not need to know the autocorrelation times, but instead only need to generate histograms which are independent. The latter is easier in practice, because independent simulations are more likely to be uncorrelated than frames *within* one simulation. I hope this helps a bit. Cheers, Jochen Am 2/19/13 3:22 PM, schrieb Steven Neumann: Dear Gmx Users, I run 10 US windows of 100 ns each - ion binding protein. I have a great convergence of profiles and good windows overlap.I tried to see PMF profiles from 10-30, 30-50, 50-70, 70-100 ns and they look very similar (Max. error would be 0.2 kcal/mol). The overal deltaG is about -5 kcal/mol. When I use g_wham with -nBootsrap 200 and -bins 200 I get error bars of -1.2 kcal/mol which is very significant. How can I impove my error bars? Why they are so large? Steven -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] removing number of sol
Hi, Then the problem lies in automating what molecules are to be removed, right? Try g_select or look into trjorder. Erik On Mar 1, 2013, at 2:45 PM, gromacs query wrote: Aha! thanks Erik (and Justin), I really feel sorry 35 and 135 will be removed by sed. I must have given a thought about that. So this was reason sed was over doing the things. Also as you asked: They are random residue number water molecules so not continuous and they were selected on the criteria based on X Y Z coordinates (some space fixed and outlier waters are to be removed) regards, On Fri, Mar 1, 2013 at 3:09 PM, Erik Marklund er...@xray.bmc.uu.se wrote: On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote: On Mar 1, 2013, at 1:58 PM, gromacs query wrote: Dear Erik, so you can filter out the unwanted residues there instead of using an index file. There are thousands of water to be removed so simple commands like sed exhausts when I run it in loops. e.g. Just to say : sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e '/ 40SOL/d' -e '/41SOL/d' -e '/42SOL/d' -e '/43SOL/d' -e '/44SOL/d' -e '/ 45SOL/d' old.gro new2.gro this will remove such 10 residues but if you run this again and again (in text exe format) say 1000 times it exhausts some how and remove waters which are not even mentioned in sed command! I have checked it many times. So I thought if index file could help me. But please reply for point 3: First of all, that's not a safe way of removing waters. Note that both SOL 35, SOL 135, ... will be removed by that command. Secondly, I'm sure you can think of a better way of scripting it, using e.g. sed or awk. By which criteria do you select the waters to be removed? If its a contiguous chunk then it's dead simple. 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . thanks, This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund er...@xray.bmc.uu.se wrote: The ndx format is really simple. You can easily script your way to a new index group as long as the selection of atoms can be automated. Furthermore, the gro format is also simple, so you can filter out the unwanted residues there instead of using an index file. Erik On Mar 1, 2013, at 1:42 PM, gromacs query wrote: Dear All, I know the residue numbers of SOL molecules (which are more than thousands) which I want to remove them from a gro file. I searched that make_ndx can be used make a index file to define residues. But It is a prompt based tool and its difficult to type manually thousands of residue numbers. 1) Is there some way to feed the residue numbers to make_ndx? Or I need to make index file format my self by some scritpting Or is there is rather easier way of doing in gromacs. 2) Also is there any direct command which helps to remove a residue number directly from a gro file without using index file input; means residue defined in command itself? 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://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 http://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read
Re: [gmx-users] do_dssp
On 3/1/13 11:16 AM, Miguel Ángel Mompeán García wrote: The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and it works fine. However, when converting the xpm to eps I get I plot very small, where one barely can see the colour code and the legend is sooo big. Does anyone know how to change that? Supply an .m2p file to xpm2ps -di to adjust the size of each matrix element. There is an example in the online manual. -Justin 2013/3/1 Erik Marklund er...@xray.bmc.uu.se What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD) in your terminal? Erik On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --**- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/**src/tools/gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read
Re: [gmx-users] GPU version of GROMACS 4.6 in MacOS cluster
Hi George, As I said before, that just means that most probably the GPU driver is not compatible with the CUDA runtime (libcudart) that you installed with the CUDA toolkit. I've no clue about the Mac OS installers and releases, you'll have to do the research on that. Let us know if you have further (GROMACS-related) issues. Cheers, -- Szilárd On Fri, Mar 1, 2013 at 2:48 PM, George Patargias g...@bioacademy.gr wrote: Hi Szilαrd Thanks for your reply. I have run the deviceQuery utility and what I got back is /deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) cudaGetDeviceCount returned 38 - no CUDA-capable device is detected Should I understand from this that the CUDA driver was not installed from the MAC OS X CUDA 5.0 Production Release? George HI, That looks like the driver does not work or is incompatible with the runtime. Please get the SDK, compile a simple program, e.g. deviceQuery and see if that works (I suspect that it won't). Regarding your machines, just FYI, the Quadro 4000 is a pretty slow card (somewhat slower than a GTX 460) so you'll hava a quite strong resource imbalance: a lot of CPU compute power (2x Xeon 5xxx, right?) and little GPU compute power which will lead to the CPU idling while waiting for the GPU. Cheers, -- Szilαrd On Thu, Feb 28, 2013 at 4:52 PM, George Patargias g...@bioacademy.grwrote: Hello We are trying to install the GPU version of GROMACS 4.6 on our own MacOS cluster. So for the cluster nodes that have the NVIDIA Quadro 4000 cards: - We have downloaded and install the MAC OS X CUDA 5.0 Production Release from here: https://developer.nvidia.com/cuda-downloads placing the libraries contained in this download in /usr/local/cuda/lib - We have managed to compile GROMACS 4.6 linking it statically with these CUDA libraries and the MPI libraries (with BUILD_SHARED_LIBS=OFF and GMX_PREFER_STATIC_LIBS=ON) Unfortunately, when we tried to run a test job with the generated mdrun_mpi, GROMACS reported that it cannot detect any CUDA-enabled devices. It also reports 0.0 version for CUDA driver and runtime. Is the actual CUDA driver missing from the MAC OS X CUDA 5.0 Production Release that we installed? Do we need to install it from here: http://www.nvidia.com/object/cuda-mac-driver.html Or is something else that we need to do? Many thanks in advance. George Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- 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 Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- 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] do_dssp
Interesting. Perhaps there are new issues with 2.1.0. Did you try to execute the command yourself? Erik On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote: The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and it works fine. However, when converting the xpm to eps I get I plot very small, where one barely can see the colour code and the legend is sooo big. Does anyone know how to change that? 2013/3/1 Erik Marklund er...@xray.bmc.uu.se What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD) in your terminal? Erik On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --**- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/**src/tools/ gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/ null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post?
Re: [gmx-users] do_dssp
Hi Erik, Since I read in the mailing list that nobody had asked about 2.1.0, just decided to try an older version before going into the trouble itself... Kind of coward, I know, but the troubles with that version are already reported so that I thought things would be easier :) Thank-you a lot for your comments 2013/3/1 Erik Marklund er...@xray.bmc.uu.se Interesting. Perhaps there are new issues with 2.1.0. Did you try to execute the command yourself? Erik On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote: The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and it works fine. However, when converting the xpm to eps I get I plot very small, where one barely can see the colour code and the legend is sooo big. Does anyone know how to change that? 2013/3/1 Erik Marklund er...@xray.bmc.uu.se What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD) in your terminal? Erik On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/ src/tools/gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Searchhttp://www.gromacs.org/**Support/Mailing_Lists/Search h**ttp://www.gromacs.org/Support/**Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Searchhttp://www.gromacs.org/**Support/Mailing_Lists/Search h**ttp://www.gromacs.org/Support/**Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read
[gmx-users] Installation Problems with Gromacs4.6
Hello Gromacs Users.
I have been trying to install Gromacs4.6 on our HPC facility. I think I
have correctly provided all the necessary mpi and fftw library paths. But
when i try to run configure it gives me the following error:
CMake Error at cmake/FindFFTW.cmake:105 (message):
Could not find fftwf_plan_r2r_1d in
/home/aacharya/softwares/fftw-3.3.3/lib/libfftw3f.so, take a look at the
error message in
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeError.log to
find out what went wrong. If you are using a static lib (.a) make sure
you
have specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
-DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):
CMakeLists.txt:894 (find_package)
As suggested here I looked into the CMakeError.log file of which I can't
make any sense.
Source file was:
#include mpi.h
int main(void) {
void* buf;
MPI_Allreduce(MPI_IN_PLACE, buf, 10, MPI_FLOAT, MPI_SUM, MPI_COMM_WORLD);
}
Determining if the function fftwf_plan_r2r_1d exists in the
/home/aacharya/softwares/fftw-3.3.3/lib failed with the following output:
Change Dir: /home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/gmake cmTryCompileExec2668319475/fast
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec2668319475.dir/build.make
CMakeFiles/cmTryCompileExec2668319475.dir/build
gmake[1]: Entering directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_progress_report
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp/CMakeFiles
1
Building C object
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d -o
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -c
/home/aacharya/softwares/cmake-2.8.10.2/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec2668319475
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_link_script
CMakeFiles/cmTryCompileExec2668319475.dir/link.txt --verbose=1
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d
-L/home/aacharya/softwares/fftw-3.3.3/lib
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -o
cmTryCompileExec2668319475 -rdynamic -lm
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o: In
function `main':
CheckFunctionExists.c:(.text+0x15): undefined reference to
`fftwf_plan_r2r_1d'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTryCompileExec2668319475] Error 1
gmake[1]: Leaving directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec2668319475/fast] Error 2
Kindly help. I tried installing 4.5.6 and it got installed without any
such problems. I need 4.6 because my tpr files are produced in Gromacs4.6
and I am using the Verlet cutoff scheme.
Thanks in advance
With Regards
Abhishek Acharya
--
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] GPU version of GROMACS 4.6 in MacOS cluster
The easiest way for solution is to kill MacOS ans switch to Linux. ;-) Albert On 03/01/2013 06:03 PM, Szilárd Páll wrote: Hi George, As I said before, that just means that most probably the GPU driver is not compatible with the CUDA runtime (libcudart) that you installed with the CUDA toolkit. I've no clue about the Mac OS installers and releases, you'll have to do the research on that. Let us know if you have further (GROMACS-related) issues. Cheers, -- Szilárd -- 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] ERROR No default G96Angle types
Dear Gromacs-Users, I am using Gromos96 43a1 FF extended to include phosphorylated residues. I have a peptide-capped with 17 aminoacids. When I tried to add ions to the virtual box I obtained these error ERROR 1 [file topol.top, line 566]: No default G96Angle types ERROR 2 [file topol.top, line 801]: No default Proper Dih. types The second error was resolved by modified the archive residuetypes.dat. I only add this line SEP Protein To be honest I don't know how to resolve the ERROR 1. If someone could help me I will appreciate. Eduardo grompp -f ions.mdp -c newbox_solv.gro -p topol.top -o ions.tpr ERROR 1 [file topol.top, line 566]: No default G96Angle types topol.top [ angles ] ; aiajak functc0c1c2 c3 1 2 3 2 newbox_solc.gro 1ACE CA1 2.759 1.040 1.830 1ACE C2 2.881 1.130 1.839 1ACE O3 2.988 1.083 1.878 2SER N4 2.872 1.258 1.805 aminoacids.rtp [ ACE ] [ atoms ] CA CH3 0.000 0 C C 0.380 1 O O -0.380 1 [ bonds ] CCA gb_26 C O gb_4 C+N gb_9 [ angles ] CA C+Nga_18 O C+Nga_32 [ impropers ] CCA+N Ogi_1 ERROR 2 [file topol.top, line 801]: No default Proper Dih. types topol.top [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 72717374 1 H N CACB newbox_sol.gro 10SEP N 71 2.348 2.562 2.883 10SEP H 72 2.446 2.556 2.863 10SEP CA 73 2.260 2.594 2.768 10SEP CB 74 2.186 2.467 2.720 10SEP OG 75 2.110 2.424 2.827 10SEP P 76 2.001 2.314 2.797 10SEPO1P 77 2.066 2.200 2.732 10SEPO2P 78 1.949 2.275 2.928 10SEPO3P 79 1.895 2.372 2.710 10SEP C 80 2.164 2.714 2.789 10SEP O 81 2.051 2.714 2.741 aminoacids.rtp [ SEP ]tar -zcvf prog-1-jan-2005.tar.gz /home/jerry/prog [ atoms ] N N-0.28000 0 H H 0.28000 0 CA CH1 0.0 1 CB CH2 0.0 2 OGOA-0.36000 2 P P 0.94000 2 O1POP-0.86000 2 O2POP-0.86000 2 O3POP-0.86000 2 C C 0.380 3 O O -0.380 3 [ bonds ] N Hgb_2 NCAgb_20 CA Cgb_26 C Ogb_4 C+Ngb_9 CACBgb_26 CBOGgb_17 OG Pgb_27 P O1Pgb_23 P O2Pgb_23 P O3Pgb_23 [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 NCA C ga_12 CA C+N ga_18 CA C O ga_29 O C+N ga_32 NCACB ga_12 CCACB ga_12 CACBOG ga_12 CBOG P ga_25 OG P O1P ga_13 OG P O2P ga_13 OG P O3P ga_13 O1P P O2P ga_28 O1P P O3P ga_28 O2P P O3P ga_28 [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CCA+N O gi_1 CA N CCB gi_2 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_4 -C NCA C gd_19 NCA C+N gd_20 NCACBOG gd_17 CACBOG P gd_14 CBOG P O1P gd_11 - Eduardo Villarreal Ramírez Postdoctoral Research Fellow Mineralized Tissue Laboratory, Hospital for Special Surgery. -- View this message in context: http://gromacs.5086.n6.nabble.com/ERROR-No-default-G96Angle-types-tp5006044.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation Problems with Gromacs4.6
On Fri, Mar 1, 2013 at 7:29 PM, Abhishek Acharya aacha...@iitk.ac.inwrote:
Hello Gromacs Users.
I have been trying to install Gromacs4.6 on our HPC facility. I think I
have correctly provided all the necessary mpi and fftw library paths.
OK, but you'll make trouble-shooting easier if you tell us what you've done
:-)
CC=mpicc cmake .. -DCMAKE_PREFIX_PATH=$HOME/softwares/fftw-3.3.3 is the
simplest form likely to work.
But
when i try to run configure it gives me the following error:
CMake Error at cmake/FindFFTW.cmake:105 (message):
Could not find fftwf_plan_r2r_1d in
/home/aacharya/softwares/fftw-3.3.3/lib/libfftw3f.so, take a look at the
error message in
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeError.log to
find out what went wrong. If you are using a static lib (.a) make sure
you
have specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
-DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):
CMakeLists.txt:894 (find_package)
As suggested here I looked into the CMakeError.log file of which I can't
make any sense.
Source file was:
#include mpi.h
int main(void) {
void* buf;
MPI_Allreduce(MPI_IN_PLACE, buf, 10, MPI_FLOAT, MPI_SUM, MPI_COMM_WORLD);
}
Determining if the function fftwf_plan_r2r_1d exists in the
/home/aacharya/softwares/fftw-3.3.3/lib failed with the following output:
Change Dir: /home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/gmake cmTryCompileExec2668319475/fast
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec2668319475.dir/build.make
CMakeFiles/cmTryCompileExec2668319475.dir/build
gmake[1]: Entering directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_progress_report
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp/CMakeFiles
1
Building C object
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d -o
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -c
/home/aacharya/softwares/cmake-2.8.10.2/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec2668319475
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_link_script
CMakeFiles/cmTryCompileExec2668319475.dir/link.txt --verbose=1
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d
-L/home/aacharya/softwares/fftw-3.3.3/lib
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -o
cmTryCompileExec2668319475 -rdynamic -lm
That looks weird. CMake is not trying to link to your FFTW library at all,
but all I can guess with current information is that something with your
call to cmake isn't working.
Mark
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o: In
function `main':
CheckFunctionExists.c:(.text+0x15): undefined reference to
`fftwf_plan_r2r_1d'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTryCompileExec2668319475] Error 1
gmake[1]: Leaving directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec2668319475/fast] Error 2
Kindly help. I tried installing 4.5.6 and it got installed without any
such problems. I need 4.6 because my tpr files are produced in Gromacs4.6
and I am using the Verlet cutoff scheme.
Thanks in advance
With Regards
Abhishek Acharya
--
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Re: [gmx-users] ERROR No default G96Angle types
On 3/1/13 3:49 PM, Villarealed wrote: Dear Gromacs-Users, I am using Gromos96 43a1 FF extended to include phosphorylated residues. I have a peptide-capped with 17 aminoacids. When I tried to add ions to the virtual box I obtained these error ERROR 1 [file topol.top, line 566]: No default G96Angle types ERROR 2 [file topol.top, line 801]: No default Proper Dih. types The second error was resolved by modified the archive residuetypes.dat. I only add this line SEP Protein To be honest I don't know how to resolve the ERROR 1. If someone could help me I will appreciate. Eduardo grompp -f ions.mdp -c newbox_solv.gro -p topol.top -o ions.tpr ERROR 1 [file topol.top, line 566]: No default G96Angle types topol.top [ angles ] ; aiajak functc0c1c2 c3 1 2 3 2 newbox_solc.gro 1ACE CA1 2.759 1.040 1.830 1ACE C2 2.881 1.130 1.839 1ACE O3 2.988 1.083 1.878 2SER N4 2.872 1.258 1.805 aminoacids.rtp [ ACE ] [ atoms ] CA CH3 0.000 0 C C 0.380 1 O O -0.380 1 [ bonds ] CCA gb_26 C O gb_4 C+N gb_9 [ angles ] CA C+Nga_18 O C+Nga_32 [ impropers ] CCA+N Ogi_1 It looks like you are using an old version of Gromacs. This was a bug that was fixed some time ago. There is a missing angle here: CA C Oga_30 ERROR 2 [file topol.top, line 801]: No default Proper Dih. types topol.top [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 72717374 1 H N CACB There should not be a dihedral assigned here. It is not specified in the .rtp, nor do the Gromos force fields assign dihedrals for H-N-X-X. The -N-CA- torsion is defined by heavy atoms only. Are you sure the numbering is correct? The numbers listed in topol.top correspond to the [moleculetype] numbering, which is not necessarily the same numbering in the coordinate file, if (for example) the residue/atom numbering does not start at 1 in the coordinate file. -Justin newbox_sol.gro 10SEP N 71 2.348 2.562 2.883 10SEP H 72 2.446 2.556 2.863 10SEP CA 73 2.260 2.594 2.768 10SEP CB 74 2.186 2.467 2.720 10SEP OG 75 2.110 2.424 2.827 10SEP P 76 2.001 2.314 2.797 10SEPO1P 77 2.066 2.200 2.732 10SEPO2P 78 1.949 2.275 2.928 10SEPO3P 79 1.895 2.372 2.710 10SEP C 80 2.164 2.714 2.789 10SEP O 81 2.051 2.714 2.741 aminoacids.rtp [ SEP ]tar -zcvf prog-1-jan-2005.tar.gz /home/jerry/prog [ atoms ] N N-0.28000 0 H H 0.28000 0 CA CH1 0.0 1 CB CH2 0.0 2 OGOA-0.36000 2 P P 0.94000 2 O1POP-0.86000 2 O2POP-0.86000 2 O3POP-0.86000 2 C C 0.380 3 O O -0.380 3 [ bonds ] N Hgb_2 NCAgb_20 CA Cgb_26 C Ogb_4 C+Ngb_9 CACBgb_26 CBOGgb_17 OG Pgb_27 P O1Pgb_23 P O2Pgb_23 P O3Pgb_23 [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 NCA C ga_12 CA C+N ga_18 CA C O ga_29 O C+N ga_32 NCACB ga_12 CCACB ga_12 CACBOG ga_12 CBOG P ga_25 OG P O1P ga_13 OG P O2P ga_13 OG P O3P ga_13 O1P P O2P ga_28 O1P P O3P ga_28 O2P P O3P ga_28 [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CCA+N O gi_1 CA N CCB gi_2 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_4 -C NCA C gd_19 NCA C+N gd_20 NCACBOG gd_17 CACBOG P gd_14 CBOG P O1P gd_11 - Eduardo Villarreal Ramírez Postdoctoral Research Fellow Mineralized Tissue Laboratory, Hospital for Special Surgery. -- View this message in context: http://gromacs.5086.n6.nabble.com/ERROR-No-default-G96Angle-types-tp5006044.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Justin A. Lemkul, Ph.D. Research Scientist 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] Re: gInstallation Problems with Gromacs4.6
Date: Fri, 1 Mar 2013 23:59:36 +0530
From: Abhishek Acharya aacha...@iitk.ac.in
Subject: [gmx-users] Installation Problems with Gromacs4.6
To: gromacs maillist gmx-users@gromacs.org
Message-ID:
2ca7063e41d6ddfa7ea411dc3cfe3ad3.squir...@webmail.iitk.ac.in
Content-Type: text/plain;charset=iso-8859-1
Hello Gromacs Users.
I have been trying to install Gromacs4.6 on our HPC facility. I think I
have correctly provided all the necessary mpi and fftw library paths. But
when i try to run configure it gives me the following error:
CMake Error at cmake/FindFFTW.cmake:105 (message):
Could not find fftwf_plan_r2r_1d in
/home/aacharya/softwares/fftw-3.3.3/lib/libfftw3f.so, take a look at the
error message in
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeError.log to
find out what went wrong. If you are using a static lib (.a) make sure
you
have specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
-DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):
CMakeLists.txt:894 (find_package)
As suggested here I looked into the CMakeError.log file of which I can't
make any sense.
Source file was:
#include mpi.h
int main(void) {
void* buf;
MPI_Allreduce(MPI_IN_PLACE, buf, 10, MPI_FLOAT, MPI_SUM, MPI_COMM_WORLD);
}
Determining if the function fftwf_plan_r2r_1d exists in the
/home/aacharya/softwares/fftw-3.3.3/lib failed with the following output:
Change Dir: /home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/gmake cmTryCompileExec2668319475/fast
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec2668319475.dir/build.make
CMakeFiles/cmTryCompileExec2668319475.dir/build
gmake[1]: Entering directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_progress_report
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp/CMakeFiles
1
Building C object
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d -o
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -c
/home/aacharya/softwares/cmake-2.8.10.2/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec2668319475
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_link_script
CMakeFiles/cmTryCompileExec2668319475.dir/link.txt --verbose=1
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d
-L/home/aacharya/softwares/fftw-3.3.3/lib
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -o
cmTryCompileExec2668319475 -rdynamic -lm
Strange, there is supposed to be a -lfftw3f before -lm. Can you
tell us what your cmake command line was?
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o: In
function `main':
CheckFunctionExists.c:(.text+0x15): undefined reference to
`fftwf_plan_r2r_1d'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTryCompileExec2668319475] Error 1
gmake[1]: Leaving directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec2668319475/fast] Error 2
Kindly help. I tried installing 4.5.6 and it got installed without any
such problems. I need 4.6 because my tpr files are produced in Gromacs4.6
and I am using the Verlet cutoff scheme.
Thanks in advance
With Regards
Abhishek Acharya
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
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Re: [gmx-users] Re: gInstallation Problems with Gromacs4.6
Date: Fri, 1 Mar 2013 23:59:36 +0530
From: Abhishek Acharya aacha...@iitk.ac.in
Subject: [gmx-users] Installation Problems with Gromacs4.6
To: gromacs maillist gmx-users@gromacs.org
Message-ID:
2ca7063e41d6ddfa7ea411dc3cfe3ad3.squir...@webmail.iitk.ac.in
Content-Type: text/plain;charset=iso-8859-1
Hello Gromacs Users.
I have been trying to install Gromacs4.6 on our HPC facility. I think I
have correctly provided all the necessary mpi and fftw library paths.
But
when i try to run configure it gives me the following error:
CMake Error at cmake/FindFFTW.cmake:105 (message):
Could not find fftwf_plan_r2r_1d in
/home/aacharya/softwares/fftw-3.3.3/lib/libfftw3f.so, take a look at
the
error message in
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeError.log
to
find out what went wrong. If you are using a static lib (.a) make
sure
you
have specified all dependencies of fftw3f in FFTWF_LIBRARY by hand
(e.g.
-DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):
CMakeLists.txt:894 (find_package)
As suggested here I looked into the CMakeError.log file of which I can't
make any sense.
Source file was:
#include mpi.h
int main(void) {
void* buf;
MPI_Allreduce(MPI_IN_PLACE, buf, 10, MPI_FLOAT, MPI_SUM,
MPI_COMM_WORLD);
}
Determining if the function fftwf_plan_r2r_1d exists in the
/home/aacharya/softwares/fftw-3.3.3/lib failed with the following
output:
Change Dir:
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/gmake cmTryCompileExec2668319475/fast
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec2668319475.dir/build.make
CMakeFiles/cmTryCompileExec2668319475.dir/build
gmake[1]: Entering directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E
cmake_progress_report
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp/CMakeFiles
1
Building C object
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d -o
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -c
/home/aacharya/softwares/cmake-2.8.10.2/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec2668319475
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_link_script
CMakeFiles/cmTryCompileExec2668319475.dir/link.txt --verbose=1
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d
-L/home/aacharya/softwares/fftw-3.3.3/lib
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -o
cmTryCompileExec2668319475 -rdynamic -lm
Strange, there is supposed to be a -lfftw3f before -lm. Can you
tell us what your cmake command line was?
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o: In
function `main':
CheckFunctionExists.c:(.text+0x15): undefined reference to
`fftwf_plan_r2r_1d'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTryCompileExec2668319475] Error 1
gmake[1]: Leaving directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec2668319475/fast] Error 2
Kindly help. I tried installing 4.5.6 and it got installed without any
such problems. I need 4.6 because my tpr files are produced in
Gromacs4.6
and I am using the Verlet cutoff scheme.
Thank you Mark and Christoph for your replies. I solved the installation
problem by configuring gromacs with static libraries. I somehow didn't
notice earlier, there was a note saying that Shared Libraries might be
problematic with MPI.
With Regards
Abhishek
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
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Re: [gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093)
Hi Justin, Thanks a lot, that suggestion of yours helped. I am on the equilibration step and its running but nothing is happening on the terminal its just stagnant. Is it fine because its more than 17 hrs now. Is there some problem. After running the second command nothing is happening on the terminal. grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr mdrun -deffnm nvt I am sorry as it is not a reasonable question to ask but i am just asking out of curiosity and lack of time. Thanks in advance. On Wed, Feb 27, 2013 at 10:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/27/13 11:14 AM, swati rana wrote: Thanx a lot that helped... but now there is one more issue. I am consulting the site for each and every error and getting most of the help but these are few which i am not able to resolve even after referring to the site. After running the energy minimization step i am facing the following error: --**- Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/**src/gmxlib/confio.c, line: 801 Fatal error: Something is wrong in the coordinate formatting of file system.gro. Note that gro is fixed format (see the manual) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors --**- I am not able to understand that in system.gro file do we have to do the change in the no of atoms according to the inflated_system.gro file or not. No, the number of atoms in the coordinate file should be correct. InflateGRO does this for you. Another thing is if i am adding Chloride ions to equalize the charge do i have to reduce the no of POPC molecules or not. Kindly suggest what should During inflation and shrinking, you should not be adding solvent or ions. You will get a nonsensical result. be done i looked into the system.gro file and also the line it is referring to i did not find anything unusual. But there is a catch its the same molecule LEU which was having link to NH3. Probably a visualization artifact. Real bonds are set in the topology, not in whatever the visualization program guesses. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
