Re: [gmx-users] Non-bonded Copper
Hi Matthew, On top of the advice of Mark, consider that Copper has a rather peculiar electronic structure, which may make it difficult to model using only a Lennard-Jones potential for the non-bonded interactions. And then it will also matter whether it's Cu(I) or Cu(II). Are you sure that the simple approach you try to take is suitable to give a good enough answer to the issue you want to address? Cheers, Tsjerk On Mon, Jun 29, 2009 at 1:45 AM, Mark Abrahammark.abra...@anu.edu.au wrote: Matthew Roode wrote: Greetings all, Let me preface this by stating I'm new at MD simulation. I am trying to perform a simulation which involves non-bonded copper atoms, amongst other things. I'm making use of the Lennard-Jones potential to describe the non-bonded interactions between them, and I've input the parameters in the ff*nb.itp file after ensuring Cu was defined in the ffgmx.atp file. I use x2top to generate the topology file, but the program stops on a fatal error telling me No forcefield type for atom Cu (841) with 0 bonds. Can any of you out there offer any advice on the cause of said error? Thus far my troubleshooting has failed. As a general rule, don't use ffgmx. Like it says in the manual and pdb2gmx, its usage is deprecated. What you need is a forcefield that models non-bonded copper. That's easier said than found. Most forcefields in common use with GROMACS are for biochemical simulations, so you may not find anything suitable already in GROMACS. Telling us your whole simulation system would have been a good idea. Likely, you'll need to search literature for a suitable model, which GROMACS is likely to be able to implement. That might require a thorough knowledge of chapter 5 of the manual. Mark ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] 4.0.5 Installation error
Hi, I am trying to install GROMACS-4.0.5, but while making mpirun with the option --enable-mpi it gives the following sets of errors: ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `ah_find' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_ksignal' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_arr_append' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `ah_delete' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_errorstr' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_ssi_cr_did' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_rtrnameget' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_mutex_trylock' ... ... The important thing to note is that I have successfully compiled and installed mpi version of mdrun on the same machine, for GROMACS-4.0.4. What am I missing here? Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: 4.0.5 Installation error
On Mon, Jun 29, 2009 at 12:54 PM, Manik Mayur manik.ma...@gmail.com wrote: Hi, I am trying to install GROMACS-4.0.5, but while making mpirun with the option --enable-mpi it gives the following sets of errors: read making mdrun ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `ah_find' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_ksignal' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_arr_append' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `ah_delete' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_errorstr' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_ssi_cr_did' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_rtrnameget' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_mutex_trylock' ... ... The important thing to note is that I have successfully compiled and installed mpi version of mdrun on the same machine, for GROMACS-4.0.4. What am I missing here? Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] 4.0.5 Installation error
Manik Mayur wrote: Hi, I am trying to install GROMACS-4.0.5, but while making mpirun with the option --enable-mpi it gives the following sets of errors: ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `ah_find' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_ksignal' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_arr_append' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `ah_delete' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_errorstr' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_ssi_cr_did' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_rtrnameget' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_mutex_trylock' ... ... The important thing to note is that I have successfully compiled and installed mpi version of mdrun on the same machine, for GROMACS-4.0.4. What am I missing here? Probably you've changed/removed your MPI library between configure and make, or between versions of GROMACS, or something similar. Unpack a clean GROMACS tarball and start again with configure. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] DSSP hangs for days
On Jun 28, 2009, at 10:46 AM, sharada wrote: Hi, I waited for it to finish for almost 5 days nothing happened except creation of those files. I had posted a similar mail some time back. Is there no solution for this. Is it something to do with speed of the system? I ran the program on HP dual core system. Hi, there were a few issues in do_dssp which I fixed recently. Could you try the most recent version from the git repository, maybe on a short trajectory first? Carsten ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] 4.0.5 Installation error
On Mon, Jun 29, 2009 at 1:51 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Manik Mayur wrote: Hi, I am trying to install GROMACS-4.0.5, but while making mpirun with the option --enable-mpi it gives the following sets of errors: ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `ah_find' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_ksignal' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_arr_append' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `ah_delete' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_errorstr' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_ssi_cr_did' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_rtrnameget' ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to `lam_mutex_trylock' ... ... The important thing to note is that I have successfully compiled and installed mpi version of mdrun on the same machine, for GROMACS-4.0.4. What am I missing here? Probably you've changed/removed your MPI library between configure and make, or between versions of GROMACS, or something similar. Unpack a clean GROMACS tarball and start again with configure. Not that I remember doing so, I will do the clean reinstall anyway. Thanks, Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] problem of getting with Dssp
Hi I want to install dssp programm in my linux machine but I am not getting it from the website http://swift.cmbi.ru.nl/gv/dssp/. The linux executable given in the website does not seems to work.Can any one suggest any alternative site for downloading the current version of dssp. Subarna Cricket on your mind? Visit the ultimate cricket website. Enter http://cricket.yahoo.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/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/mailing_lists/users.php
Re: [gmx-users] problem of getting with Dssp
I did not test it, but ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip offers the sources and what I see from the readme.txt, it doesn't seem difficult to compile it yourself. -- ### Volker Wirth Center for Medical Physics and Technology Biophysics Group FAU Erlangen-Nuremberg Email: vwirth%at%biomed.uni-erlangen.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/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/mailing_lists/users.php
Re: [gmx-users] DSSP hangs for days
On Jun 29, 2009, at 11:58 AM, sharada wrote: hello, I have downloaded the tar file from the github and extracted the contents. However I am unable to understand the README file as it is in a language other than english. Could you kindly provide the instructions how to go about using it. Hi, If you have git installed, all you need to do to download the Gromacs sources is git clone git://git.gromacs.org/gromacs.git If there is no git installed on your machine, there are also rpm files provided on git-scm.com/download. Everything should be in english there I would guess. Carsten ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] SD temperature coupling groups
Hi GROMACS user group! Maybe this should be aimed at the developers' mailing list... Anyway, I've been having some problems (blowing up) when I tried to simulate a molecule such that one part is coupled to a thermal bath using SD, and another part is not coupled to any bath. Effectively, the uncoupled part has infinite relaxation time (tau-T) which is the same as zero coupling (gamma); however, in the *.mdp file it is unrealistic to put in the value infinity for the tau-T parameter. The 4.0 manual specifically says, in section 7.3.14, Temperature coupling: tau t: [ps] time constant for coupling (one for each group in tc grps), 0 means no temperature coupling However, when I tried putting in zero I got the following (debugging information log-file) line 267: SD const tc-grp 0: b nan c inf d -inf line 268: SD const tc-grp 1: b 2.08438e-14 c 8.33021e-11 d -2.5e-07 where group 0 had tau-T[0] = 0 and group 1 had tau-T[0] = 1 ps . This shows that when I put zero in the temperature coupling timescale (for SD this is not exactly a first-order relaxation time), the SD parameters blow up. Note that when I put tau-T[0] = 1000 or tau-T[0] = 1, the simulation ran properly. Where in the code can I check that what is written in the manual is, indeed correct? (i.e., I expect an if statement saying that if the tau-T value of some temperature coupling group is zero, then take the inverse of that to be effectively zero). Thanks in advance, -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail.___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] protonation state with pdb2gmx
Hello, with pdb2gmx I want to choose the protonation state of a GLN interactively. When I choose +1 protonation state, I get the following error: Residue 'QLN' not found in residue topology database. But the program has itself suggested the QLN as the name of this protonation state!! Would be pleased by your comments! cheers, Peyman Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] protonation state with pdb2gmx
Yamin, Peyman wrote: Hello, with pdb2gmx I want to choose the protonation state of a GLN interactively. When I choose +1 protonation state, I get the following error: Residue 'QLN' not found in residue topology database. But the program has itself suggested the QLN as the name of this protonation state!! Then you've chosen a force field for which the name QLN simply doesn't apply :) In fact, the only force field with QLN is OPLS. -Justin Would be pleased by your comments! cheers, Peyman Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
AW: [gmx-users] protonation state with pdb2gmx
OH! And a (-1) Alanine I can never have since pdb2gmx has no option for that? It's my C-Terminus in the end! :-| Von: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] im Auftrag von Justin A. Lemkul [jalem...@vt.edu] Gesendet: Montag, 29. Juni 2009 16:53 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] protonation state with pdb2gmx Yamin, Peyman wrote: Hello, with pdb2gmx I want to choose the protonation state of a GLN interactively. When I choose +1 protonation state, I get the following error: Residue 'QLN' not found in residue topology database. But the program has itself suggested the QLN as the name of this protonation state!! Then you've chosen a force field for which the name QLN simply doesn't apply :) In fact, the only force field with QLN is OPLS. -Justin Would be pleased by your comments! cheers, Peyman Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Artificial Shear Flow and Inconsistent Shift Error
Hi All, 1. Artificial Shear Flow: I am trying to do translocation studies and wanted to generate a shear flow without actual water atoms. I checked the mail list and it was mentioned that there is no velocity profile but an option to accelerate the atoms in a group. But I wanted to get the shear flow or the velocity profile without atoms. To make myself clear: I want the boat to navigate through water, with the flow of water but there is no water, am I making sense? So I want an artificial force applied constantly in the channel not on the particle so basically I define the velocity profile using the artificial force. 2. Inconsistent Shifts Error: I received this error in my simulation studies when I used PBC =xyz There were XXX inconsistent shifts. Check your topology , checked the mail-list and found the option of pbc = full should be used, but seems it is not available anymore in gromacs 4.0.3, My system is very small around 1000 atoms, and it works fine without periodic conditions, but when pbc is added it runs for some time and then gives me the error. What does this error actually mean? How can I resolve this? Regards, Aby ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] disable ulimit
Hi Gustavo,
On Jun 24, 2009, at 20:48 , Gustavo Fioravanti wrote:
we are trying to run mdrun_mpi in a public cluster of our
university. However, we got the following error:
/etc/profile.d/limits.sh: line 1: ulimit: max locked memory: cannot
modify limit: Operation not permitted
There are two kinds of ulimits, soft and hard. Hard limits cannot be
increased, so maybe you try to exceed a hard limit here?
/var/tmp/sge_local_spool/r01n19/job_scripts/3051: line 10:
grompp_mpi: command not found
The cluster has already settled to unlimited access to memory.
However, grompp hasn't have permission to modify this file
(limits.sh).
I do not think grompp tries to modify the file. The error message
above seems to point at limits.sh not being allowed to raise the
limit. Did you talk to your sysadmin? They should be able to raise the
limit. BTW, note that the limit in question here is not memory per se,
but locked memory.
I would like to disable the ulimit function at source file from
GROMACS. How can I do that?
Try to do it from a script (or by hand) before starting gromacs, like
so:
ulimit -l unlimited
Modifying the limit from the program is also possible, but a little
bit more involved (this code should work on Linux; on other systems,
things might be a bit different):
#include sys/resource.h
struct rlimit unlim = {RLIM_INFINITY, RLIM_INFINITY};
int err = setrlimit(RLIMIT_MEMLOCK, unlim);
/* error handling skeleton; based on the error message given above,
you will probably get EPERM */
if (err)
switch (errno)
{
case EFAULT: /* limit points outside address range */
break;
case EINVAL: /* invalid resource, or soft hard */
break;
case EPERM: /* unprivileged process tried to raise hard limit */
break;
}
A.
--
Ansgar Esztermann
DV-Systemadministration
Max-Planck-Institut für biophysikalische Chemie, Abteilung 105
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[gmx-users] Making sure I understand an error
Hi, I have a 72-lipid DPPC (MARTINI) system that I ran for 400ns in GROMACS 3.3.3. I picked a snapshot from the middle (~100ns), so I know it should be equilibrated and be able to run for several hundred nanoseconds. If I use GROMACS 4.0.3 (or 4.0.5) and 1, 2, or 4 processors, everything is great. However, if I use more than 4 processors (either on a single node or on two nodes), I get errors like this: - begin error - vol 0.87 imb F 2% step 350900, will finish Sat Jun 27 23:16:51 2009 vol 0.84 imb F 4% step 351000, will finish Sat Jun 27 23:16:49 2009 A list of missing interactions: G96Angle of576 missing 1 Molecule type 'DPP' the first 10 missing interactions, except for exclusions: G96Angle atoms235 global 254 255 257 --- Program mdrun_mpi, VERSION 4.0.5 Source code file: domdec_top.c, line: 341 Fatal error: 1 of the 1368 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck --- Pump Up the Volume Along With the Tempo (Jazzy Jeff) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 8 gcq#177: Pump Up the Volume Along With the Tempo (Jazzy Jeff) h199:0.MPID_Abort: h199:0.MPI Abort by user Aborting program ! h199:0.MPID_CH_Abort: h199:0.Aborting program! Abort on node h199 due to MPI_Abort (type 2) -- end error -- This error happens on a different step depending on how many processors I use, whether I use gfortran or ifort, etc. Am I understanding correctly that I have a triplet of particles A-B-C where the bond-angle term cannot be calculated because the distance between A and C is greater than 1.2 nm? Is dynamic load balancing causing the error to happen at different steps for different numbers of processors? It appears that I can fix the problem by setting -rdd=1.4 on the command line, but I'd like to make sure I'm not just sweeping something else under the rug. For what it's worth, the equilibrium bond lengths in MARTINI's DPPC model are all either .47 or .37 nm. In the -rdd=1.4 run, the maximum bond lengths range from .68 to .71 nm depending on the particular bond and the A-C distances from the A-B-C triplets range from 1.09 to 1.21. Also, is there any chance that the default settings will get this right for my system in the future? Thanks, -michael -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Making sure I understand an error
You are right. With MARTINI you often need an rdd bigger than default. 1.4 is reasonable. On Jun 29, 2009, at 19:33, Michael Lerner mglerner+grom...@gmail.com wrote: Hi, I have a 72-lipid DPPC (MARTINI) system that I ran for 400ns in GROMACS 3.3.3. I picked a snapshot from the middle (~100ns), so I know it should be equilibrated and be able to run for several hundred nanoseconds. If I use GROMACS 4.0.3 (or 4.0.5) and 1, 2, or 4 processors, everything is great. However, if I use more than 4 processors (either on a single node or on two nodes), I get errors like this: - begin error - vol 0.87 imb F 2% step 350900, will finish Sat Jun 27 23:16:51 2009 vol 0.84 imb F 4% step 351000, will finish Sat Jun 27 23:16:49 2009 A list of missing interactions: G96Angle of576 missing 1 Molecule type 'DPP' the first 10 missing interactions, except for exclusions: G96Angle atoms235 global 254 255 257 --- Program mdrun_mpi, VERSION 4.0.5 Source code file: domdec_top.c, line: 341 Fatal error: 1 of the 1368 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck --- Pump Up the Volume Along With the Tempo (Jazzy Jeff) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 8 gcq#177: Pump Up the Volume Along With the Tempo (Jazzy Jeff) h199:0.MPID_Abort: h199:0.MPI Abort by user Aborting program ! h199:0.MPID_CH_Abort: h199:0.Aborting program! Abort on node h199 due to MPI_Abort (type 2) -- end error -- This error happens on a different step depending on how many processors I use, whether I use gfortran or ifort, etc. Am I understanding correctly that I have a triplet of particles A-B- C where the bond-angle term cannot be calculated because the distance between A and C is greater than 1.2 nm? Is dynamic load balancing causing the error to happen at different steps for different numbers of processors? It appears that I can fix the problem by setting -rdd=1.4 on the command line, but I'd like to make sure I'm not just sweeping something else under the rug. For what it's worth, the equilibrium bond lengths in MARTINI's DPPC model are all either .47 or .37 nm. In the -rdd=1.4 run, the maximum bond lengths range from .68 to .71 nm depending on the particular bond and the A-C distances from the A-B-C triplets range from 1.09 to 1.21. Also, is there any chance that the default settings will get this right for my system in the future? Thanks, -michael -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] What method (algorimth) is used to calculate volume of a protein?
Hi everybody, I used g_sas command in Gromacs4.0.3 to calculate volume of a protein. I read Gromacs4_manual and found information on internet to understand method(algorithm) used in Gromacs to calculate volume of a protein (or a system consisting of water and protein). But I can not find the solution. I think the method bases on Voronoi construction, but I am not sure. Can you tell me what method(algorithm) is used in Gromacs4 to calculate the volumes. Thank you in advance. Best wish, MHViet ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Conversion of units to nm in .xyz or pdb
hello gromacs users, I am working with a silica structure which is parallepiped in structure, i.e the unit cell is 46.4207 37.7846 18.9596 angles =90, 90, 120 I have a structure file in .xyz and .pdb but the units are in Angstroms and for gromacs I assume that I need to convert these units to nm? This is where I am encountering problems. I have tried simply dividing the atomic coordinates and cell lengths by a factor of 10 but the resulting structure doesnt look right in vmd. Do I need to use some sort of symmetry transformation to take the non-cubic symmetry into account when scaling the coordinates? Is there some program (either within gromacs or external) which will convert atomic coordinates from Angstroms to nm while carrying out the necessary symmetry operations? Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Conversion of units to nm in .xyz or pdb
Jennifer Williams wrote: hello gromacs users, I am working with a silica structure which is parallepiped in structure, i.e the unit cell is 46.4207 37.7846 18.9596 angles =90, 90, 120 I have a structure file in .xyz and .pdb but the units are in Angstroms and for gromacs I assume that I need to convert these units to nm? This is where I am encountering problems. You do not need to make any conversion. Gromacs can handle .pdb files just fine. I have tried simply dividing the atomic coordinates and cell lengths by a factor of 10 but the resulting structure doesnt look right in vmd. Do I need to use some sort of symmetry transformation to take the non-cubic symmetry into account when scaling the coordinates? Is there some program (either within gromacs or external) which will convert atomic coordinates from Angstroms to nm while carrying out the necessary symmetry operations? Simply dividing by 10 may have altered the formatting of your file. There are certain formatting standards that must be adhered to in structure files. But as I said above, .pdb format is just fine. -Justin Thanks -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
[gmx-users] the warning about the -rerun
hi,gmx-users， I want to calculate the interaction energy between two group. So I modify the .mdp file as follows: energygrps = Protein sol and make tpr file: grompp -f md.mdp -c out.gro -p topol.top -o rerun.tpr -n index.ndx mdrun -rerun md.trr -s rerun.tpr -o rerun.trr -c rerun.gro -e rerun.edr -g rerun.log It gives warings: WARNING: Some frames do not contain velocities. Ekin, temperature and pressure are incorrect, the virial will be incorrect when constraints are present. How can I deal with the warning? Jinyao Wang wan...@ciac.jl.cn 2009-06-30 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Installation with non standard location of fftw3
Hi, I have to install gromacs on a 30 node cluster computer. I only have access to a specific space on the cluster, and it didn't have fftw3 installed on it. I have installed it, and set the CPPFLAGS and LDFLAGS environment variables as per instructions. The include and lib directories exist, and the environment variables are correct. When I tried to install without fftw3 installed I got the following: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Other alternatives are 'fftw2', or 'mkl' for Intel MKL. You are STRONGLY recommended to use one of these - fftw is free. Use CPPFLAGS and LDFLAGS if the library is installed in a non-standard location. (see FAQ at http://www.gromacs.org) Now with the environment variables set I get: checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library fftw3 is installed in /hpc/software/packages/chemistry/fftw The export commands are: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-I/hpc/software/packages/chemistry/fftw/lib as per installation documentation: * GROMACS tries to find FFTW and all optional libraries (like Lesstif and FFTW) automatically, but this requires that they are present in the default places where the system searches for include files and libraries. If this is not the case (for instance, your system might not look in /usr/local/include and /usr/local/lib where FFTW is placed) you can tell configure to include these catalogues by using the variables CPPFLAGS and LDFLAGS for includes and libraries, respectively. For instance, assume we have installed FFTW with --prefix=/home/joe/fftw. ... or, if you are using a bash shell: * export CPPFLAGS=-I/home/joe/fftw/include export LDFLAGS=-L/home/joe/fftw/lib Both of these directories exist, and the fftw install seemed to run without errors. Any help would be greatly appreciated, as I am running out of ideas. I have tried to find the faq page, but without success. Thanks. Cheers, Graham Kettlewell Research assistant Centre for Atmospheric Chemistry University of Wollongong grah...@uow.edu.au Tel: (61 2) 4221 5120 Fax: (61 2) 4221 4287 Mob: 0414 309 524 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Installation with non standard location of fftw3
Graham Kettlewell wrote: Hi, I have to install gromacs on a 30 node cluster computer. I only have access to a specific space on the cluster, and it didn't have fftw3 installed on it. I have installed it, and set the CPPFLAGS and LDFLAGS environment variables as per instructions. The include and lib directories exist, and the environment variables are correct. When I tried to install without fftw3 installed I got the following: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Other alternatives are 'fftw2', or 'mkl' for Intel MKL. You are STRONGLY recommended to use one of these - fftw is free. Use CPPFLAGS and LDFLAGS if the library is installed in a non-standard location. (see FAQ at http://www.gromacs.org) Now with the environment variables set I get: checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library fftw3 is installed in /hpc/software/packages/chemistry/fftw The export commands are: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-I/hpc/software/packages/chemistry/fftw/lib You want this line to contain -L, not -I. -Justin as per installation documentation: * GROMACS tries to find FFTW and all optional libraries (like Lesstif and FFTW) automatically, but this requires that they are present in the default places where the system searches for include files and libraries. If this is not the case (for instance, your system might not look in /usr/local/include and /usr/local/lib where FFTW is placed) you can tell configure to include these catalogues by using the variables CPPFLAGS and LDFLAGS for includes and libraries, respectively. For instance, assume we have installed FFTW with --prefix=/home/joe/fftw. ... or, if you are using a bash shell: * export CPPFLAGS=-I/home/joe/fftw/include export LDFLAGS=-L/home/joe/fftw/lib Both of these directories exist, and the fftw install seemed to run without errors. Any help would be greatly appreciated, as I am running out of ideas. I have tried to find the faq page, but without success. Thanks. Cheers, Graham Kettlewell Research assistant Centre for Atmospheric Chemistry University of Wollongong grah...@uow.edu.au Tel: (61 2) 4221 5120 Fax: (61 2) 4221 4287 Mob: 0414 309 524 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
Re: [gmx-users] Installation with non standard location of fftw3
Justin A. Lemkul wrote: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-I/hpc/software/packages/chemistry/fftw/lib You want this line to contain -L, not -I. That may have been a bit unclear; the LDFLAGS line should use -L, your CPPFLAGS line is fine. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
RE: [gmx-users] Installation with non standard location of fftw3
Hi Justin, Thanks for your quick reply. It turns out that the stuff I posted was malformed, as you pointed out, but it was a desperate attempt after a number of goes, and I got that one wrong. I tried again using: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-L/hpc/sofware/packages/chemistry/fftw/lib -sh-3.2$ echo $CPPFLAGS -I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ echo $LDFLAGS -L/hpc/sofware/packages/chemistry/fftw/lib Is still got: checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library exactly as before. I am kicking myself for posting the malformed stuff. Any ideas? Cheers, Graham Kettlewell Research assistant Centre for Atmospheric Chemistry University of Wollongong grah...@uow.edu.au Tel: (61 2) 4221 5120 Fax: (61 2) 4221 4287 Mob: 0414 309 524 -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, 30 June 2009 1:25 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Installation with non standard location of fftw3 Justin A. Lemkul wrote: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-I/hpc/software/packages/chemistry/fftw/lib You want this line to contain -L, not -I. That may have been a bit unclear; the LDFLAGS line should use -L, your CPPFLAGS line is fine. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Installation with non standard location of fftw3
Graham Kettlewell wrote: Hi Justin, Thanks for your quick reply. It turns out that the stuff I posted was malformed, as you pointed out, but it was a desperate attempt after a number of goes, and I got that one wrong. I tried again using: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-L/hpc/sofware/packages/chemistry/fftw/lib -sh-3.2$ echo $CPPFLAGS -I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ echo $LDFLAGS -L/hpc/sofware/packages/chemistry/fftw/lib Is still got: checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library exactly as before. I am kicking myself for posting the malformed stuff. Any ideas? How did you install FFTW? What are the contents of the /lib directory? -Justin Cheers, Graham Kettlewell Research assistant Centre for Atmospheric Chemistry University of Wollongong grah...@uow.edu.au Tel: (61 2) 4221 5120 Fax: (61 2) 4221 4287 Mob: 0414 309 524 -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, 30 June 2009 1:25 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Installation with non standard location of fftw3 Justin A. Lemkul wrote: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-I/hpc/software/packages/chemistry/fftw/lib You want this line to contain -L, not -I. That may have been a bit unclear; the LDFLAGS line should use -L, your CPPFLAGS line is fine. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
RE: [gmx-users] Installation with non standard location of fftw3
-Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, 30 June 2009 1:57 PM To: Gromacs Users' List Subject: Re: [gmx-users] Installation with non standard location of fftw3 Graham Kettlewell wrote: Hi Justin, Thanks for your quick reply. It turns out that the stuff I posted was malformed, as you pointed out, but it was a desperate attempt after a number of goes, and I got that one wrong. I tried again using: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-L/hpc/sofware/packages/chemistry/fftw/lib -sh-3.2$ echo $CPPFLAGS -I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ echo $LDFLAGS -L/hpc/sofware/packages/chemistry/fftw/lib Is still got: checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library exactly as before. I am kicking myself for posting the malformed stuff. Any ideas? How did you install FFTW? What are the contents of the /lib directory? I installed fftw3.2.1 using the tarball. As I remember it was: tar -xzvf fftw-3.2.1.tar.gz mkdir ../fftw cd fftw-3.2.1 ./configure --prefix /hpc/software/packages/chemistry/fftw make make install I retyped this, so... The contents of lib are: -sh-3.2$ cd lib/ -sh-3.2$ ls -l total 2196 -rw-r--r-- 1 grahamk uowstf 2230376 Jun 30 10:02 libfftw3.a -rwxr-xr-x 1 grahamk uowstf 951 Jun 30 10:02 libfftw3.la drwxr-xr-x 2 grahamk uowstf4096 Jun 30 10:02 pkgconfig Cheers, graham -Justin Cheers, Graham Kettlewell Research assistant Centre for Atmospheric Chemistry University of Wollongong grah...@uow.edu.au Tel: (61 2) 4221 5120 Fax: (61 2) 4221 4287 Mob: 0414 309 524 -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, 30 June 2009 1:25 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Installation with non standard location of fftw3 Justin A. Lemkul wrote: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-I/hpc/software/packages/chemistry/fftw/lib You want this line to contain -L, not -I. That may have been a bit unclear; the LDFLAGS line should use -L, your CPPFLAGS line is fine. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Installation with non standard location of fftw3
Graham Kettlewell wrote: -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, 30 June 2009 1:57 PM To: Gromacs Users' List Subject: Re: [gmx-users] Installation with non standard location of fftw3 Graham Kettlewell wrote: Hi Justin, Thanks for your quick reply. It turns out that the stuff I posted was malformed, as you pointed out, but it was a desperate attempt after a number of goes, and I got that one wrong. I tried again using: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-L/hpc/sofware/packages/chemistry/fftw/lib -sh-3.2$ echo $CPPFLAGS -I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ echo $LDFLAGS -L/hpc/sofware/packages/chemistry/fftw/lib Is still got: checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library exactly as before. I am kicking myself for posting the malformed stuff. Any ideas? How did you install FFTW? What are the contents of the /lib directory? I installed fftw3.2.1 using the tarball. As I remember it was: tar -xzvf fftw-3.2.1.tar.gz mkdir ../fftw cd fftw-3.2.1 ./configure --prefix /hpc/software/packages/chemistry/fftw make make install I retyped this, so... The contents of lib are: -sh-3.2$ cd lib/ -sh-3.2$ ls -l total 2196 -rw-r--r-- 1 grahamk uowstf 2230376 Jun 30 10:02 libfftw3.a -rwxr-xr-x 1 grahamk uowstf 951 Jun 30 10:02 libfftw3.la drwxr-xr-x 2 grahamk uowstf4096 Jun 30 10:02 pkgconfig OK, that explains it. You don't have the libfftwf.a and libfftwf.la that the configure script is looking for. The recommended installation procedure (creating single- and double-precision versions) is: ./configure --enable-threads --enable-float make make install make distclean ./configure --enable-threads make make install -Justin Cheers, graham -Justin Cheers, Graham Kettlewell Research assistant Centre for Atmospheric Chemistry University of Wollongong grah...@uow.edu.au Tel: (61 2) 4221 5120 Fax: (61 2) 4221 4287 Mob: 0414 309 524 -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, 30 June 2009 1:25 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Installation with non standard location of fftw3 Justin A. Lemkul wrote: -sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include -sh-3.2$ export LDFLAGS=-I/hpc/software/packages/chemistry/fftw/lib You want this line to contain -L, not -I. That may have been a bit unclear; the LDFLAGS line should use -L, your CPPFLAGS line is fine. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
