Re: [gmx-users] Re:g_clustsize problem
Wang Zhun wrote: Hi, David, The command I use is g_cluster -f traj.trr -s topol.tpr -cutoff 0.2 -minstruct 2 -o rmsd-clust.xpm -g cluster.log choose group 1 Protein This is fine, results look OK. So what's the problem? and g_clustsize -f traj.trr -o csize.xpm -cut 0.2 -n index.ndx choose group 1 Protein This is not meaningful. the following is part of cluster log which says 12 clusters found rather than 1 cluster: Using linkage method for clustering Using RMSD cutoff 0.2 nm The RMSD ranges from 0.0738896 to 2.25219 nm Average RMSD is 0.61356 Number of structures for matrix 4001 Energy of the matrix is 1004.6 nm Found 12 clusters cl. | #st rmsd | middle rmsd | cluster members 1 | 1 | 0 | 0 2 | 8 .612 | 5 .271 | 5 10 15 20 25 30 35 | | | 40 3 | 21.084 | 45 .169 | 45 50 4 | 141.636 | 55 .292 | 55 60 65 70 75 80 85 | | | 90 95100105110115120 5 | 32.092 |125 .197 |125130135 6 | 132.640 |140 .292 |140145150155160165170 | | |175180185190195200 7 | 313.199 |205 .433 |205210215220225230235 | | |240245250255260265270 | | |275280285290295300305 | | |310315320325330335340 | | |345350355 8 | 23.572 |360 .143 |360365 9 | 74.119 |370 .264 |370375380385390395400 10 | 124.633 |405 .283 |405410415420425430435 | | |440445450455460 11 | 325.164 |465 .356 |465470475480485490495 | | |500505510515520525530 | | |535540545550555560565 | | |570575580585590595600 | | |605610615620 12 | 38765.784 |810 .806 |625630635640645650655 | | |660665670675680685690 | | |695700705710715720725 | | |730735740745750755760 | | |765770775780785790795 | | |800805810815820825830 | | |835840845850855860865 | | |870875880885890895900 | | |905910915920925930935 | | |940945950955960965970 // ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error
Gaurav Chopra wrote: Hi I am doing a steepest descent for the initial mdrun for a peptide and it gives me the following error. Please advice. Thanks Gaurav --- Program mdrun, VERSION 3.3 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Please follow the advice in the above two sentences. Check your structure. Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ] Please report this to the mailing list (gmx-users@gromacs.org) --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] xtc files
YOLANDA SMALL wrote: Hi All, How do I convert xtc files exported for a subset of atoms in my system to pdb files? When I run trjconv, I get the following error message: Fatal error: Index[0] 3611 is larger than the number of atoms in the trajectory file (3152) In my mdp file I specify the option 'xtc_grps' to export a subset of solvent and protein atoms to an xtc file. This subset of atoms is defined in my index file and contains 3152 atoms. Then I discard the .trr files to save space. It looks like the atom index gets renumbered from 1 in the new .xtc file so that the new atom indeces no longer correspond to the atoms in the original coordinate file. How do I recover the coordinates with matching atom names from the .xtc file? Sorry I misread your question. You make a pdb file from your original tpr using the same index group you used for the xtc-grps, then you use this pdb file as reference for trjconv on the xtc to pdb conversion. Thanks, Yolanda ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] xtc files
YOLANDA SMALL wrote: Hi All, How do I convert xtc files exported for a subset of atoms in my system to pdb files? When I run trjconv, I get the following error message: Fatal error: Index[0] 3611 is larger than the number of atoms in the trajectory file (3152) In my mdp file I specify the option 'xtc_grps' to export a subset of solvent and protein atoms to an xtc file. This subset of atoms is defined in my index file and contains 3152 atoms. Then I discard the .trr files to save space. It looks like the atom index gets renumbered from 1 in the new .xtc file so that the new atom indeces no longer correspond to the atoms in the original coordinate file. How do I recover the coordinates with matching atom names from the .xtc file? you need to make an inverse index files. First you had a selection 1 --> 1 3 --> 2 5 --> 3 7 --> 4 11 --> 5 13 --> 6 Now you have to generate the inverse of your xtc-grp Thanks, Yolanda ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] keep atoms planar
hello, i found in ffoplsaa.itp : [ dihedraltypes ] ; Improper OPLS dihedrals to keep groups planar. ; (OPLS doesnt use impropers for chiral atoms). ; Since these functions are periodic of the form 1-cos(2*x), the are actually ; implemented as proper dihedrals [1+cos(2*x+180)] for the moment, ; to keep things compatible. ; The defines are used in ffoplsaa.rtp or directly in your .top ile. ; O?-C -X -Y improper torsion. C can be C_2 or C_3 too. #define improper_O_C_X_Y180.0 43.93200 2 ; X-NO-ON-NO improper torsion. #define improper_X_NO_ON_NO 180.0 43.93200 2 ; N2-X-N2-N2 improper torsion. #define improper_N2_X_N2_N2 180.0 43.93200 2 ; Z -N?-X -Y improper torsion #define improper_Z_N_X_Y180.0 4.18400 2 ; Z -CM-X -Y improper torsion. CM can be C= too. #define improper_Z_CM_X_Y 180.0 62.76000 2 ; Z -CA-X -Y improper torsion. CA is any ring carbon (CA,CB,CN,CV,CW,CR,CK,CQ,CS,C*) #define improper_Z_CA_X_Y 180.0 4.60240 2 are X Y Z designate any atom types? -- Rongliang Wu 2006-03-14 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:g_clustsize problem
Hi, David, The command I use is g_cluster -f traj.trr -s topol.tpr -cutoff 0.2 -minstruct 2 -o rmsd-clust.xpm -g cluster.log choose group 1 Protein and g_clustsize -f traj.trr -o csize.xpm -cut 0.2 -n index.ndx choose group 1 Protein the following is part of cluster log which says 12 clusters found rather than 1 cluster: Using linkage method for clustering Using RMSD cutoff 0.2 nm The RMSD ranges from 0.0738896 to 2.25219 nm Average RMSD is 0.61356 Number of structures for matrix 4001 Energy of the matrix is 1004.6 nm Found 12 clusters cl. | #st rmsd | middle rmsd | cluster members 1 | 1 | 0 | 0 2 | 8 .612 | 5 .271 | 5 10 15 20 25 30 35 | | | 40 3 | 21.084 | 45 .169 | 45 50 4 | 141.636 | 55 .292 | 55 60 65 70 75 80 85 | | | 90 95100105110115120 5 | 32.092 |125 .197 |125130135 6 | 132.640 |140 .292 |140145150155160165170 | | |175180185190195200 7 | 313.199 |205 .433 |205210215220225230235 | | |240245250255260265270 | | |275280285290295300305 | | |310315320325330335340 | | |345350355 8 | 23.572 |360 .143 |360365 9 | 74.119 |370 .264 |370375380385390395400 10 | 124.633 |405 .283 |405410415420425430435 | | |440445450455460 11 | 325.164 |465 .356 |465470475480485490495 | | |500505510515520525530 | | |535540545550555560565 | | |570575580585590595600 | | |605610615620 12 | 38765.784 |810 .806 |625630635640645650655 | | |660665670675680685690 | | |695700705710715720725 | | |730735740745750755760 | | |765770775780785790795 | | |800805810815820825830 | | |835840845850855860865 | | |870875880885890895900 | | |905910915920925930935 | | |940945950955960965970 // ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] xtc files
YOLANDA SMALL wrote: Hi All, How do I convert xtc files exported for a subset of atoms in my system to pdb files? When I run trjconv, I get the following error message: Fatal error: Index[0] 3611 is larger than the number of atoms in the trajectory file (3152) In my mdp file I specify the option 'xtc_grps' to export a subset of solvent and protein atoms to an xtc file. This subset of atoms is defined in my index file and contains 3152 atoms. Then I discard the .trr files to save space. It looks like the atom index gets renumbered from 1 in the new .xtc file so that the new atom indeces no longer correspond to the atoms in the original coordinate file. Did you use -shuffle -sort? Even in such case, the renumbering won't take number larger than the total number of atoms. You may have selected the group in the index file which includes all the atoms. More information from you is appreciated. P.S.: Use gmxcheck -f to check how many atoms inside the xtc. How do I recover the coordinates with matching atom names from the .xtc file? Thanks, Yolanda ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] xtc files
Hi All, How do I convert xtc files exported for a subset of atoms in my system to pdb files? When I run trjconv, I get the following error message: Fatal error: Index[0] 3611 is larger than the number of atoms in the trajectory file (3152) In my mdp file I specify the option 'xtc_grps' to export a subset of solvent and protein atoms to an xtc file. This subset of atoms is defined in my index file and contains 3152 atoms. Then I discard the .trr files to save space. It looks like the atom index gets renumbered from 1 in the new .xtc file so that the new atom indeces no longer correspond to the atoms in the original coordinate file. How do I recover the coordinates with matching atom names from the .xtc file? Thanks, Yolanda ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Rychaert-Belleman's dihedral
hello all, i'm using the opls force field to simulate a system of molecules with benzene ring, i found the default dihedral fun is 3(Rychaert-Belleman's dihedral), and do i have to add those dihedrals in the benzene to the [ impropers ] so as to insure the atoms are in a plane? or can the "fun 3" keep the stoms of the benzene within the plane? is it necessary to use Rychaert-Belleman's dihedral for the oplsaa force filed? Regards! -- Rongliang Wu 2006-03-14 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Range checking error
Hi I am doing a steepest descent for the initial mdrun for a peptide and it gives me the following error. Please advice. Thanks Gaurav --- Program mdrun, VERSION 3.3 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ] Please report this to the mailing list (gmx-users@gromacs.org) --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Why my protein always falls out of the water box?
Shanjie Huang wrote: Hi dear friends, I performed a molecular dynamics of a ligand-receptor complex for 5ns; but I found that my complex always fall out from the water box quickly in the first 1ns. What may be the problem? Can I constrain some residues which are far away from the active site to aviod this problem? But I am worry about the extra constrain would interfere my MD result, for in the normal situation there should be no constrains. Thanks. When using comm-grps= Protein in your mdp file the center of mass of you protein will stay at its starting position. good luck, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Why my protein always falls out of the water box?
Hi you!it may not be as bad as it looks like. Usually the one happening to your protein is only a visualization problem, if an atom of your protein crosses the periodic simulation box, it might appear as if the whole molecule jumps out of the box, because the coordinates of one of its periodic images are shown instead of those referring to the real box. You can simply assess if this is the case by running a single step dynamics, at a low temperature, if the protein jumps out all the same, it can't be because of the real protein movement! In this case, you can just convert you trajectory by trjconv -center -pbc wholethis way you should have a trajectory in which your protein quietly stays in its box.hope it helps!greetings,MGiòOn 3/13/06, Shanjie Huang <[EMAIL PROTECTED]> wrote: Hi dear friends,I performed a molecular dynamics of a ligand-receptor complex for 5ns;but I found that my complex always fall out from the water box quicklyin the first 1ns. What may be the problem?Can I constrain some residues which are far away from the active site to aviod this problem? But I am worry about the extra constrain wouldinterfere my MD result, for in the normal situation there should be noconstrains.Thanks.-- Shanjie Huang [EMAIL PROTECTED]--http://www.fastmail.fm - A no graphics, no pop-ups email service___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Why my protein always falls out of the water box?
Hi dear friends, I performed a molecular dynamics of a ligand-receptor complex for 5ns; but I found that my complex always fall out from the water box quickly in the first 1ns. What may be the problem? Can I constrain some residues which are far away from the active site to aviod this problem? But I am worry about the extra constrain would interfere my MD result, for in the normal situation there should be no constrains. Thanks. -- Shanjie Huang [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] can not write a gro file without atom names
Do you want to create a really short trajectory with only two frames, or do you want to create a structure with both structures given in your gro files in it? In the latter case, turn you gro files into pdb (editconf), use "cat a.pdb b.pdb > c.pdb" and remove the ENDMDL and TER lines by hand. Jochen Viswanadham Sridhara wrote: Hi everyone, I am trying to concatenate two .gro files obtained from two separate trajcetories. It says "can not write a gro file without atom names" with trjcat command. Any suggestions or any more info you required?? Thanks, -Viswam. -- Viswanadham Sridhara, Graduate Research Assistant, Old Dominion University, "VIRGINIA". ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 23, Issue 34
> > > 1. Does anybody have a 'ready-to-run' topology > > for SW water (the polarisable water model from J.Phys. Chem. > > B (2001), 105, 2618? > > As I see the sw.itp in the standart distribution > > has improper order of directives. Am I right or it is just > > the Friday night and I should take a rest for a while...? > > http://www.gromacs.org/pipermail/gmx-users/2003-December/008346.html > Great! Thanks a lot, Dallas. I was almost sure that it should be something like this: a simple but not-so-obvious mistake :-). All the best, Maxim. > Catch ya, > > Dr. Dallas Warren > Lecturer > Department of Pharmaceutical Biology and Pharmacology > Victorian College of Pharmacy, Monash University > 381 Royal Parade, Parkville VIC 3010 > [EMAIL PROTECTED] > +61 3 9903 9524 > - > When the only tool you own is a hammer, every problem begins to > resemblea nail. > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Gromacs3.3 Compilation on IBM powerpc
Dear Erik:
The last error is just "configure:6705: error: cannot compute sizeof
(int), 77"
Xie Yinghong
> Find the _last_ error in config.log, and check what the compiler
said > about it.> Cheers,> ErikOn
Mar 14, 2006, at 2:11 AM, Yinghong wrote:> Dear
Erik:>> I have carefully read through config.log
file, and I found out some > possible problems for
compilation failure, could you please help me > to locate
the real reason and solution?>> As I think, maybe
this error is from xlc, but it seemed much > related to
"conftest.c" file, which was reported for several times > as
errors.>> How should I deal it with? By the way, I
have passed through the > compilation of single version. The
following errors were from MPI > compilation. Of course, I
only added a "--enable-mpi" flag when > compling MPI
version, as described in the last
email.>>> config.log:>
...> ...> ...> ## ---
##> ## Core tests. ##> ## ---
##> ...> ...> configure:2586: checking
for C compiler version> configure:2589: xlc --version
&5> xlc: 1501-216 command option --version
is not recognized - passed > to ld>
...> ...> ...> configure:2806:
checking whether we are using the GNU C compiler> configure:2830:
xlc -c -O3 -qarch=pwr4 -qtune=pwr4 -qansialias -w - >
I/afs/ipp-garching.mpg.de/home/x/xieyh/fftw_213/include conftest.c
>&5> "conftest.c", line 20.14: 1506-275 (S) Unexpected text
me encountered.> "conftest.c", line 20.8: 1506-045 (S) Undeclared
identifier choke.> configure:2836: $? = 1>
configure: failed program was:> | /* confdefs.h.
*/> |> | #define PACKAGE_NAME
"GROMACS"> | #define PACKAGE_TARNAME "gromacs"> |
#define PACKAGE_VERSION "3.3"> | #define PACKAGE_STRING "GROMACS
3.3"> | #define PACKAGE_BUGREPORT "gmx-users at
gromacs.org"> | #define PACKAGE "gromacs"> |
#define VERSION "3.3"> | #define GMX_SOFTWARE_SQRT>
| #define BUILD_TIME "Mon Mar 13 08:13:33 NFT 2006"> | #define
BUILD_USER "xieyh at
psi24"> | #define BUILD_MACHINE "AIX 2
0010594A4C00"> | /* end confdefs.h. */>
|> | int> | main ()> |
{> | #ifndef __GNUC__>
| choke me> |
#endif> |> | ;>
| return 0;> | }>>
configure:2889: xlc -c -g -I/afs/ipp-garching.mpg.de/home/x/xieyh/
> fftw_213/include conftest.c >&5>
configure:2895: $? = 0> configure:2899: test
-z>
|| test ! -s conftest.err> ...> ...>
configure:3061: xlc -c -O3 -qarch=pwr4 -qtune=pwr4 -qansialias -w -
> I/afs/ipp-garching.mpg.de/home/x/xieyh/fftw_213/include
conftest.c >&5> "conftest.c", line 2.3: 1506-166 (S)
Definition of function choke > requires
parentheses.> "conftest.c", line 2.9: 1506-046 (S) Syntax
error.> configure:3067: $? = 1> configure: failed
program was:> | #ifndef __cplusplus> |
choke me> | #endif> ...>
...> configure:4775: mpcc -E
-I/afs/ipp-garching.mpg.de/home/x/xieyh/ > fftw_213/include
conftest.c> "conftest.c", line 18.10: 1506-296 (S) #include
file > not found.>
...> ...> | #include >
| #include > | #ifdef
F77_DUMMY_MAIN> |> | # ifdef
__cplusplus> | extern
"C"> | # endif> | int
F77_DUMMY_MAIN() { return 1; }> |> |
#endif> | int> | main ()> |
{> |> | FILE *f = fopen ("conftest.val",
"w");> | if (! f)>
| exit (1);> | if (((long)
(sizeof (int))) < 0)> |
{> | long i = longval
();> | if (i != ((long)
(sizeof (int> | exit
(1);> | fprintf (f, "%ld\n",
i);> | }> |
else> | {>
| unsigned long i = ulongval
();> | if (i != ((long)
(sizeof (int> | exit
(1);> | fprintf (f, "%lu\n",
i);> | }> | exit
(ferror (f) || fclose (f) != 0);> |> |
;> | return 0;> | }>
configure:6705: error: cannot compute sizeof (int), 77> See
`config.log' for more
details. Xie
Yinghong
Hi, Check config.log for the actual error.
You might also want to make>> sure that you can compile a small
MPI test program.
Cheers,
Erik On Mar 13, 2006, at 8:52 PM, Yinghong
wrote:> Dear
users:>> I have successfully
installed fftw2.1.3 and single version>>> Gromacs3.3 on IBM
powerpc Aix5.2.0.0 with the following>>> environmental
variables:>> setenv CC
xlc>>> setenv MPICC mpcc>>> setenv F77
xlf>>> setenv CXX xlC>>> setenv CPPFLAGS
-I.../fftw_213/include>>> setenv LDFLAGS
-L.../fftw_213/lib>>> setenv CFLAGS "-O3 -qarch=pwr4
-qtune=pwr4 -qansialias -w">>> setenv FFLAGS "-O3
-qarch=pwr4 -qtune=pwr4 -qansialias -qstrict -w">>> Now, I
would like to compile the parallel version of Gromacs3.3,>>>
and I did it as the follows:>>> 1. make
disclean;>>> 2. ./configure --prefix=$HOME/gromacs33
--exec-prefix=$HOME/>>> gromacs33 --enable-float
--disable-fortran --disable-largefile -->>> without-x
--disable->>> vectorized-sqrt --with-fft=fftw2 --enable-mpi
--program-suffix=_mpi>> It is worthy
noting that the all parameters for ./configure are the>>>
same as perviously successful single version, except that
"--enable->>> mpi --program-suffix=_mpi" is
Re: [gmx-users] Re: Gromacs3.3 Compilation on IBM powerpc
Find the _last_ error in config.log, and check what the compiler said
about it.
Cheers,
Erik
On Mar 14, 2006, at 2:11 AM, Yinghong wrote:
Dear Erik:
I have carefully read through config.log file, and I found out some
possible problems for compilation failure, could you please help me
to locate the real reason and solution?
As I think, maybe this error is from xlc, but it seemed much
related to "conftest.c" file, which was reported for several times
as errors.
How should I deal it with? By the way, I have passed through the
compilation of single version. The following errors were from MPI
compilation. Of course, I only added a "--enable-mpi" flag when
compling MPI version, as described in the last email.
config.log:
...
...
...
## --- ##
## Core tests. ##
## --- ##
...
...
configure:2586: checking for C compiler version
configure:2589: xlc --version &5
xlc: 1501-216 command option --version is not recognized - passed
to ld
...
...
...
configure:2806: checking whether we are using the GNU C compiler
configure:2830: xlc -c -O3 -qarch=pwr4 -qtune=pwr4 -qansialias -w -
I/afs/ipp-garching.mpg.de/home/x/xieyh/fftw_213/include conftest.c >&5
"conftest.c", line 20.14: 1506-275 (S) Unexpected text me encountered.
"conftest.c", line 20.8: 1506-045 (S) Undeclared identifier choke.
configure:2836: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "GROMACS"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "3.3"
| #define PACKAGE_STRING "GROMACS 3.3"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE "gromacs"
| #define VERSION "3.3"
| #define GMX_SOFTWARE_SQRT
| #define BUILD_TIME "Mon Mar 13 08:13:33 NFT 2006"
| #define BUILD_USER "[EMAIL PROTECTED]"
| #define BUILD_MACHINE "AIX 2 0010594A4C00"
| /* end confdefs.h. */
|
| int
| main ()
| {
| #ifndef __GNUC__
|choke me
| #endif
|
| ;
| return 0;
| }
configure:2889: xlc -c -g -I/afs/ipp-garching.mpg.de/home/x/xieyh/
fftw_213/include conftest.c >&5
configure:2895: $? = 0
configure:2899: test -z
|| test ! -s conftest.err
...
...
configure:3061: xlc -c -O3 -qarch=pwr4 -qtune=pwr4 -qansialias -w -
I/afs/ipp-garching.mpg.de/home/x/xieyh/fftw_213/include conftest.c >&5
"conftest.c", line 2.3: 1506-166 (S) Definition of function choke
requires parentheses.
"conftest.c", line 2.9: 1506-046 (S) Syntax error.
configure:3067: $? = 1
configure: failed program was:
| #ifndef __cplusplus
| choke me
| #endif
...
...
configure:4775: mpcc -E -I/afs/ipp-garching.mpg.de/home/x/xieyh/
fftw_213/include conftest.c
"conftest.c", line 18.10: 1506-296 (S) #include file
not found.
...
...
| #include
| #include
| #ifdef F77_DUMMY_MAIN
|
| # ifdef __cplusplus
| extern "C"
| # endif
|int F77_DUMMY_MAIN() { return 1; }
|
| #endif
| int
| main ()
| {
|
| FILE *f = fopen ("conftest.val", "w");
| if (! f)
| exit (1);
| if (((long) (sizeof (int))) < 0)
| {
| long i = longval ();
| if (i != ((long) (sizeof (int
| exit (1);
| fprintf (f, "%ld\n", i);
| }
| else
| {
| unsigned long i = ulongval ();
| if (i != ((long) (sizeof (int
| exit (1);
| fprintf (f, "%lu\n", i);
| }
| exit (ferror (f) || fclose (f) != 0);
|
| ;
| return 0;
| }
configure:6705: error: cannot compute sizeof (int), 77
See `config.log' for more details.
Xie Yinghong
Hi,
Check config.log for the actual error. You might also want to make
sure that you can compile a small MPI test program.
Cheers,
Erik
On Mar 13, 2006, at 8:52 PM, Yinghong wrote:
Dear users:
I have successfully installed fftw2.1.3 and single version
Gromacs3.3 on IBM powerpc Aix5.2.0.0 with the following
environmental variables:
setenv CC xlc
setenv MPICC mpcc
setenv F77 xlf
setenv CXX xlC
setenv CPPFLAGS -I.../fftw_213/include
setenv LDFLAGS -L.../fftw_213/lib
setenv CFLAGS "-O3 -qarch=pwr4 -qtune=pwr4 -qansialias -w"
setenv FFLAGS "-O3 -qarch=pwr4 -qtune=pwr4 -qansialias -qstrict -w"
Now, I would like to compile the parallel version of Gromacs3.3,
and I did it as the follows:
1. make disclean;
2. ./configure --prefix=$HOME/gromacs33 --exec-prefix=$HOME/
gromacs33 --enable-float --disable-fortran --disable-largefile --
without-x --disable-
vectorized-sqrt --with-fft=fftw2 --enable-mpi --program-suffix=_mpi
It is worthy noting that the all parameters for ./configure are the
same as perviously successful single version, except that "--enable-
mpi --program-suffix=_mpi" is added in compiling MPI version.
However, compilation can not pass because of the following reason.
If anybody encountered such an error, could you give me some
suggestion? How to deal with it? Any help will be extermely
appreciately.
...
...
checking for style of include used by make... GNU
checking dependency style of xlc... none
checking for mpxlc... mpcc
checking whether the MPI cc command works... yes
checking how to run
[gmx-users] Re: Gromacs3.3 Compilation on IBM powerpc
Dear Erik:
I have carefully read through config.log file, and I found out some possible
problems for compilation failure, could you please help me to locate the real
reason and solution?
As I think, maybe this error is from xlc, but it seemed much related to
"conftest.c" file, which was reported for several times as errors.
How should I deal it with? By the way, I have passed through the compilation of
single version. The following errors were from MPI compilation. Of course, I
only added a "--enable-mpi" flag when compling MPI version, as described in the
last email.
config.log:
...
...
...
## --- ##
## Core tests. ##
## --- ##
...
...
configure:2586: checking for C compiler version
configure:2589: xlc --version &5
xlc: 1501-216 command option --version is not recognized - passed to ld
...
...
...
configure:2806: checking whether we are using the GNU C compiler
configure:2830: xlc -c -O3 -qarch=pwr4 -qtune=pwr4 -qansialias -w
-I/afs/ipp-garching.mpg.de/home/x/xieyh/fftw_213/include conftest.c >&5
"conftest.c", line 20.14: 1506-275 (S) Unexpected text me encountered.
"conftest.c", line 20.8: 1506-045 (S) Undeclared identifier choke.
configure:2836: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "GROMACS"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "3.3"
| #define PACKAGE_STRING "GROMACS 3.3"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE "gromacs"
| #define VERSION "3.3"
| #define GMX_SOFTWARE_SQRT
| #define BUILD_TIME "Mon Mar 13 08:13:33 NFT 2006"
| #define BUILD_USER "[EMAIL PROTECTED]"
| #define BUILD_MACHINE "AIX 2 0010594A4C00"
| /* end confdefs.h. */
|
| int
| main ()
| {
| #ifndef __GNUC__
|choke me
| #endif
|
| ;
| return 0;
| }
configure:2889: xlc -c -g
-I/afs/ipp-garching.mpg.de/home/x/xieyh/fftw_213/include conftest.c >&5
configure:2895: $? = 0
configure:2899: test -z
|| test ! -s conftest.err
...
...
configure:3061: xlc -c -O3 -qarch=pwr4 -qtune=pwr4 -qansialias -w
-I/afs/ipp-garching.mpg.de/home/x/xieyh/fftw_213/include conftest.c >&5
"conftest.c", line 2.3: 1506-166 (S) Definition of function choke requires
parentheses.
"conftest.c", line 2.9: 1506-046 (S) Syntax error.
configure:3067: $? = 1
configure: failed program was:
| #ifndef __cplusplus
| choke me
| #endif
...
...
configure:4775: mpcc -E
-I/afs/ipp-garching.mpg.de/home/x/xieyh/fftw_213/include conftest.c
"conftest.c", line 18.10: 1506-296 (S) #include file not
found.
...
...
| #include
| #include
| #ifdef F77_DUMMY_MAIN
|
| # ifdef __cplusplus
| extern "C"
| # endif
|int F77_DUMMY_MAIN() { return 1; }
|
| #endif
| int
| main ()
| {
|
| FILE *f = fopen ("conftest.val", "w");
| if (! f)
| exit (1);
| if (((long) (sizeof (int))) < 0)
| {
| long i = longval ();
| if (i != ((long) (sizeof (int
| exit (1);
| fprintf (f, "%ld\n", i);
| }
| else
| {
| unsigned long i = ulongval ();
| if (i != ((long) (sizeof (int
| exit (1);
| fprintf (f, "%lu\n", i);
| }
| exit (ferror (f) || fclose (f) != 0);
|
| ;
| return 0;
| }
configure:6705: error: cannot compute sizeof (int), 77
See `config.log' for more details.
Xie Yinghong
>Hi,
>
>Check config.log for the actual error. You might also want to make
>sure that you can compile a small MPI test program.
>
>Cheers,
>
>Erik
>
>On Mar 13, 2006, at 8:52 PM, Yinghong wrote:
>
>> Dear users:
>>
>> I have successfully installed fftw2.1.3 and single version
>> Gromacs3.3 on IBM powerpc Aix5.2.0.0 with the following
>> environmental variables:
>>
>> setenv CC xlc
>> setenv MPICC mpcc
>> setenv F77 xlf
>> setenv CXX xlC
>> setenv CPPFLAGS -I.../fftw_213/include
>> setenv LDFLAGS -L.../fftw_213/lib
>> setenv CFLAGS "-O3 -qarch=pwr4 -qtune=pwr4 -qansialias -w"
>> setenv FFLAGS "-O3 -qarch=pwr4 -qtune=pwr4 -qansialias -qstrict -w"
>> Now, I would like to compile the parallel version of Gromacs3.3,
>> and I did it as the follows:
>> 1. make disclean;
>> 2. ./configure --prefix=$HOME/gromacs33 --exec-prefix=$HOME/
>> gromacs33 --enable-float --disable-fortran --disable-largefile --
>> without-x --disable-
>> vectorized-sqrt --with-fft=fftw2 --enable-mpi --program-suffix=_mpi
>>
>> It is worthy noting that the all parameters for ./configure are the
>> same as perviously successful single version, except that "--enable-
>> mpi --program-suffix=_mpi" is added in compiling MPI version.
>> However, compilation can not pass because of the following reason.
>> If anybody encountered such an error, could you give me some
>> suggestion? How to deal with it? Any help will be extermely
>> appreciately.
>>
>> ...
>> ...
>> checking for style of include used by make... GNU
>> checking dependency style of xlc... none
>> checking for mpxlc... mpcc
>> checking whether the MPI cc command works... yes
>> checking how to run the C preprocessor... mpc
Re: [gmx-users] Gromacs3.3 Compilation on IBM powerpc
Hi, Check config.log for the actual error. You might also want to make sure that you can compile a small MPI test program. Cheers, Erik On Mar 13, 2006, at 8:52 PM, Yinghong wrote: Dear users: I have successfully installed fftw2.1.3 and single version Gromacs3.3 on IBM powerpc Aix5.2.0.0 with the following environmental variables: setenv CC xlc setenv MPICC mpcc setenv F77 xlf setenv CXX xlC setenv CPPFLAGS -I.../fftw_213/include setenv LDFLAGS -L.../fftw_213/lib setenv CFLAGS "-O3 -qarch=pwr4 -qtune=pwr4 -qansialias -w" setenv FFLAGS "-O3 -qarch=pwr4 -qtune=pwr4 -qansialias -qstrict -w" Now, I would like to compile the parallel version of Gromacs3.3, and I did it as the follows: 1. make disclean; 2. ./configure --prefix=$HOME/gromacs33 --exec-prefix=$HOME/ gromacs33 --enable-float --disable-fortran --disable-largefile -- without-x --disable- vectorized-sqrt --with-fft=fftw2 --enable-mpi --program-suffix=_mpi It is worthy noting that the all parameters for ./configure are the same as perviously successful single version, except that "--enable- mpi --program-suffix=_mpi" is added in compiling MPI version. However, compilation can not pass because of the following reason. If anybody encountered such an error, could you give me some suggestion? How to deal with it? Any help will be extermely appreciately. ... ... checking for style of include used by make... GNU checking dependency style of xlc... none checking for mpxlc... mpcc checking whether the MPI cc command works... yes checking how to run the C preprocessor... mpcc -E ** * Using CFLAGS from environment variable * ** checking whether byte ordering is bigendian... yes checking for egrep... grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for int... yes checking size of int... configure: error: cannot compute sizeof (int), 77 See `config.log' for more details. Xie Yinghong Hong Kong University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_clustsize problem
Wang Zhun wrote: Hi, I'm working on peptide folding with GMX3.2.1 now. When I carried out g_clustsize, it says: Group 1 ( Protein) has 211 elements Group 2 ( Protein-H) has 167 elements Group 3 ( C-alpha) has22 elements Group 4 (Backbone) has66 elements Group 5 ( MainChain) has89 elements Group 6 (MainChain+Cb) has 108 elements Group 7 ( MainChain+H) has 112 elements Group 8 ( SideChain) has99 elements Group 9 ( SideChain-H) has78 elements Group10 ( Prot-Masses) has 211 elements Group11 ( Non-Protein) has 20439 elements Group12 ( SOL) has 20439 elements Group13 ( Other) has 20439 elements Select a group: 1 Selected 1: 'Protein' Last frame 4000 time 2.000 cmid: 1, cmax: 1, max_size: 211 Fatal error: Lo: 0.00, Mid: 1.00, Hi: 1.00 What's the meaning of the last two lines? there is only one cluster, which is logical since you have one molecule. you probably want to use g_cluster Thank you in advance! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
