Re: [gmx-users] Run test in parallel
Dear Yang, Thank you for your corporation. Regards, Teru 2008/8/7 Yang Ye <[EMAIL PROTECTED]>: > ikedaike wrote: >> >> Dear Yang, >> >> Thank you for your quick reply. >> >> I checked the log files and then found that the mpirun command cannot >> find the mdrun(executable) file.. >> I modified to use the absolute path in the gmxtest.pl and ran it. >> However some tests still failed. >> >> % ./gmxtest.pl -np 8 all >> Will test on 8 processors >> FAILED. Check files in angles125 >> 1 out of 16 simple tests FAILED >> FAILED. Check files in dec+water >> No topol.tpr file in fe_test. grompp failed >> FAILED. Check files in fe_test >> 2 out of 14 complex tests FAILED >> All 63 kernel tests PASSED >> Error not all 45 pdb2gmx tests have been done successfully >> Only 0 energies in the log file >> >> Can I ignore above error messages? >> > > Most likely. I checked those errors before and they are indeed not errors. > gmxtest suite is not just not very up-to-date with gromacs. >> >> Thank you in advance. >> >> Regards, >> Teru >> >> 2008/8/7 Yang Ye <[EMAIL PROTECTED]>: >> >>> >>> I would guess that you have got gromacs installed correctly from the >>> two-process tests. >>> >>> The failure of eight-core test may depends how you start your MPI daemon >>> or other factors that mdrun could be not running at all. Paste your log >>> file from eight-core test or just wait for some one has experience with >>> OpenMPI. >>> >>> Regards, >>> Yang Ye >>> >>> ikedaike wrote: >>> Hi I built GROMACS-3.3.3 with GCC-3.4.6 and OpenMPI-1.2.5 on CentOS 4.5(Intel Core2 Duo). I tested with gmxtest-3.3.3 and all tests passed in non-parallel. However, when I tested in parallel, I encountered the following messages. [Use 2 Cores] % ./gmxtest.pl -np 2 all Will test on 2 processors All 16 simple tests PASSED FAILED. Check files in dec+water 1 out of 14 complex tests FAILED All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file Can I ignore above messages about the pdb2gmx test? [Use 8 Cores] % ./gmxtest.pl -np 8 all Will test on 8 processors FAILED. Check files in angles1 FAILED. Check files in angles125 FAILED. Check files in bham FAILED. Check files in bonds1 FAILED. Check files in bonds125 FAILED. Check files in dih1 FAILED. Check files in dih125 FAILED. Check files in g96angles1 FAILED. Check files in g96angles125 FAILED. Check files in g96bonds1 FAILED. Check files in g96bonds125 FAILED. Check files in imp1 FAILED. Check files in imp36 FAILED. Check files in morse FAILED. Check files in rb1 FAILED. Check files in rb125 16 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in aminoacids FAILED. Check files in argon FAILED. Check files in butane FAILED. Check files in dec+water FAILED. Check files in ethyleenglycol No topol.tpr file in fe_test. grompp failed FAILED. Check files in fe_test FAILED. Check files in field FAILED. Check files in nacl FAILED. Check files in sw FAILED. Check files in tip4p FAILED. Check files in tip4pflex FAILED. Check files in urea FAILED. Check files in water 14 out of 14 complex tests FAILED FAILED. Check files in kernel010 FAILED. Check files in kernel020 FAILED. Check files in kernel030 FAILED. Check files in kernel100 FAILED. Check files in kernel101 FAILED. Check files in kernel102 FAILED. Check files in kernel103 FAILED. Check files in kernel104 FAILED. Check files in kernel110 FAILED. Check files in kernel111 FAILED. Check files in kernel112 FAILED. Check files in kernel113 FAILED. Check files in kernel114 FAILED. Check files in kernel120 FAILED. Check files in kernel121 FAILED. Check files in kernel122 FAILED. Check files in kernel123 FAILED. Check files in kernel124 FAILED. Check files in kernel130 FAILED. Check files in kernel131 FAILED. Check files in kernel132 FAILED. Check files in kernel133 FAILED. Check files in kernel134 FAILED. Check files in kernel200 FAILED. Check files in kernel201 FAILED. Check files in kernel202 FAILED. Check files in kernel203 FAILED. Check files in kernel204 FAILED. Check files in kernel210 FAILED. Check files in kernel211 FAILED. Check files in kernel212 FAILED. Check files in kernel213 FAILED. Check files in kernel214 FAILED. Check files in kernel220 FAILED. Check files in kernel221 FAILED. Check files in kernel222 FAILED. Check files in kernel223 FAILED. Check files in kernel224 FAILED. Check files in kernel230 FAILED. Check files in kernel231 FAILED. Check files in kernel232 FAILE
Re: [gmx-users] Run test in parallel
ikedaike wrote: Dear Yang, Thank you for your quick reply. I checked the log files and then found that the mpirun command cannot find the mdrun(executable) file.. I modified to use the absolute path in the gmxtest.pl and ran it. However some tests still failed. % ./gmxtest.pl -np 8 all Will test on 8 processors FAILED. Check files in angles125 1 out of 16 simple tests FAILED FAILED. Check files in dec+water No topol.tpr file in fe_test. grompp failed FAILED. Check files in fe_test 2 out of 14 complex tests FAILED All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file Can I ignore above error messages? Most likely. I checked those errors before and they are indeed not errors. gmxtest suite is not just not very up-to-date with gromacs. Thank you in advance. Regards, Teru 2008/8/7 Yang Ye <[EMAIL PROTECTED]>: I would guess that you have got gromacs installed correctly from the two-process tests. The failure of eight-core test may depends how you start your MPI daemon or other factors that mdrun could be not running at all. Paste your log file from eight-core test or just wait for some one has experience with OpenMPI. Regards, Yang Ye ikedaike wrote: Hi I built GROMACS-3.3.3 with GCC-3.4.6 and OpenMPI-1.2.5 on CentOS 4.5(Intel Core2 Duo). I tested with gmxtest-3.3.3 and all tests passed in non-parallel. However, when I tested in parallel, I encountered the following messages. [Use 2 Cores] % ./gmxtest.pl -np 2 all Will test on 2 processors All 16 simple tests PASSED FAILED. Check files in dec+water 1 out of 14 complex tests FAILED All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file Can I ignore above messages about the pdb2gmx test? [Use 8 Cores] % ./gmxtest.pl -np 8 all Will test on 8 processors FAILED. Check files in angles1 FAILED. Check files in angles125 FAILED. Check files in bham FAILED. Check files in bonds1 FAILED. Check files in bonds125 FAILED. Check files in dih1 FAILED. Check files in dih125 FAILED. Check files in g96angles1 FAILED. Check files in g96angles125 FAILED. Check files in g96bonds1 FAILED. Check files in g96bonds125 FAILED. Check files in imp1 FAILED. Check files in imp36 FAILED. Check files in morse FAILED. Check files in rb1 FAILED. Check files in rb125 16 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in aminoacids FAILED. Check files in argon FAILED. Check files in butane FAILED. Check files in dec+water FAILED. Check files in ethyleenglycol No topol.tpr file in fe_test. grompp failed FAILED. Check files in fe_test FAILED. Check files in field FAILED. Check files in nacl FAILED. Check files in sw FAILED. Check files in tip4p FAILED. Check files in tip4pflex FAILED. Check files in urea FAILED. Check files in water 14 out of 14 complex tests FAILED FAILED. Check files in kernel010 FAILED. Check files in kernel020 FAILED. Check files in kernel030 FAILED. Check files in kernel100 FAILED. Check files in kernel101 FAILED. Check files in kernel102 FAILED. Check files in kernel103 FAILED. Check files in kernel104 FAILED. Check files in kernel110 FAILED. Check files in kernel111 FAILED. Check files in kernel112 FAILED. Check files in kernel113 FAILED. Check files in kernel114 FAILED. Check files in kernel120 FAILED. Check files in kernel121 FAILED. Check files in kernel122 FAILED. Check files in kernel123 FAILED. Check files in kernel124 FAILED. Check files in kernel130 FAILED. Check files in kernel131 FAILED. Check files in kernel132 FAILED. Check files in kernel133 FAILED. Check files in kernel134 FAILED. Check files in kernel200 FAILED. Check files in kernel201 FAILED. Check files in kernel202 FAILED. Check files in kernel203 FAILED. Check files in kernel204 FAILED. Check files in kernel210 FAILED. Check files in kernel211 FAILED. Check files in kernel212 FAILED. Check files in kernel213 FAILED. Check files in kernel214 FAILED. Check files in kernel220 FAILED. Check files in kernel221 FAILED. Check files in kernel222 FAILED. Check files in kernel223 FAILED. Check files in kernel224 FAILED. Check files in kernel230 FAILED. Check files in kernel231 FAILED. Check files in kernel232 FAILED. Check files in kernel233 FAILED. Check files in kernel234 FAILED. Check files in kernel300 FAILED. Check files in kernel301 FAILED. Check files in kernel302 FAILED. Check files in kernel303 FAILED. Check files in kernel304 FAILED. Check files in kernel310 FAILED. Check files in kernel311 FAILED. Check files in kernel312 FAILED. Check files in kernel313 FAILED. Check files in kernel314 FAILED. Check files in kernel320 FAILED. Check files in kernel321 FAILED. Check files in kernel322 FAILED. Check files in kernel323 FAILED. Check files in kernel324 FAILED. Check files in kernel330 FAILED. Check files in kernel331 FAILED. Check files in kernel332 FAILED. Check files in kernel333 FAILED. Check files in kernel334 63
Re: [gmx-users] Run test in parallel
Dear Yang, Thank you for your quick reply. I checked the log files and then found that the mpirun command cannot find the mdrun(executable) file.. I modified to use the absolute path in the gmxtest.pl and ran it. However some tests still failed. % ./gmxtest.pl -np 8 all Will test on 8 processors FAILED. Check files in angles125 1 out of 16 simple tests FAILED FAILED. Check files in dec+water No topol.tpr file in fe_test. grompp failed FAILED. Check files in fe_test 2 out of 14 complex tests FAILED All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file Can I ignore above error messages? Thank you in advance. Regards, Teru 2008/8/7 Yang Ye <[EMAIL PROTECTED]>: > I would guess that you have got gromacs installed correctly from the > two-process tests. > > The failure of eight-core test may depends how you start your MPI daemon > or other factors that mdrun could be not running at all. Paste your log > file from eight-core test or just wait for some one has experience with > OpenMPI. > > Regards, > Yang Ye > > ikedaike wrote: >> >> Hi >> >> I built GROMACS-3.3.3 with GCC-3.4.6 and OpenMPI-1.2.5 on CentOS >> 4.5(Intel Core2 Duo). >> I tested with gmxtest-3.3.3 and all tests passed in non-parallel. >> However, when I tested in parallel, I encountered the following messages. >> >> [Use 2 Cores] >> % ./gmxtest.pl -np 2 all >> Will test on 2 processors >> All 16 simple tests PASSED >> FAILED. Check files in dec+water >> 1 out of 14 complex tests FAILED >> All 63 kernel tests PASSED >> Error not all 45 pdb2gmx tests have been done successfully >> Only 0 energies in the log file >> >> Can I ignore above messages about the pdb2gmx test? >> >> [Use 8 Cores] >> % ./gmxtest.pl -np 8 all >> Will test on 8 processors >> FAILED. Check files in angles1 >> FAILED. Check files in angles125 >> FAILED. Check files in bham >> FAILED. Check files in bonds1 >> FAILED. Check files in bonds125 >> FAILED. Check files in dih1 >> FAILED. Check files in dih125 >> FAILED. Check files in g96angles1 >> FAILED. Check files in g96angles125 >> FAILED. Check files in g96bonds1 >> FAILED. Check files in g96bonds125 >> FAILED. Check files in imp1 >> FAILED. Check files in imp36 >> FAILED. Check files in morse >> FAILED. Check files in rb1 >> FAILED. Check files in rb125 >> 16 out of 16 simple tests FAILED >> FAILED. Check files in acetonitrilRF >> FAILED. Check files in aminoacids >> FAILED. Check files in argon >> FAILED. Check files in butane >> FAILED. Check files in dec+water >> FAILED. Check files in ethyleenglycol >> No topol.tpr file in fe_test. grompp failed >> FAILED. Check files in fe_test >> FAILED. Check files in field >> FAILED. Check files in nacl >> FAILED. Check files in sw >> FAILED. Check files in tip4p >> FAILED. Check files in tip4pflex >> FAILED. Check files in urea >> FAILED. Check files in water >> 14 out of 14 complex tests FAILED >> FAILED. Check files in kernel010 >> FAILED. Check files in kernel020 >> FAILED. Check files in kernel030 >> FAILED. Check files in kernel100 >> FAILED. Check files in kernel101 >> FAILED. Check files in kernel102 >> FAILED. Check files in kernel103 >> FAILED. Check files in kernel104 >> FAILED. Check files in kernel110 >> FAILED. Check files in kernel111 >> FAILED. Check files in kernel112 >> FAILED. Check files in kernel113 >> FAILED. Check files in kernel114 >> FAILED. Check files in kernel120 >> FAILED. Check files in kernel121 >> FAILED. Check files in kernel122 >> FAILED. Check files in kernel123 >> FAILED. Check files in kernel124 >> FAILED. Check files in kernel130 >> FAILED. Check files in kernel131 >> FAILED. Check files in kernel132 >> FAILED. Check files in kernel133 >> FAILED. Check files in kernel134 >> FAILED. Check files in kernel200 >> FAILED. Check files in kernel201 >> FAILED. Check files in kernel202 >> FAILED. Check files in kernel203 >> FAILED. Check files in kernel204 >> FAILED. Check files in kernel210 >> FAILED. Check files in kernel211 >> FAILED. Check files in kernel212 >> FAILED. Check files in kernel213 >> FAILED. Check files in kernel214 >> FAILED. Check files in kernel220 >> FAILED. Check files in kernel221 >> FAILED. Check files in kernel222 >> FAILED. Check files in kernel223 >> FAILED. Check files in kernel224 >> FAILED. Check files in kernel230 >> FAILED. Check files in kernel231 >> FAILED. Check files in kernel232 >> FAILED. Check files in kernel233 >> FAILED. Check files in kernel234 >> FAILED. Check files in kernel300 >> FAILED. Check files in kernel301 >> FAILED. Check files in kernel302 >> FAILED. Check files in kernel303 >> FAILED. Check files in kernel304 >> FAILED. Check files in kernel310 >> FAILED. Check files in kernel311 >> FAILED. Check files in kernel312 >> FAILED. Check files in kernel313 >> FAILED. Check files in kernel314 >> FAILED. Check files in kernel320 >> FAILED. Check files in kernel321 >> FAILED. Check files in kernel322 >> FAILED. Check files in kernel323 >> FAILED.
Re: [gmx-users] Run test in parallel
I would guess that you have got gromacs installed correctly from the two-process tests. The failure of eight-core test may depends how you start your MPI daemon or other factors that mdrun could be not running at all. Paste your log file from eight-core test or just wait for some one has experience with OpenMPI. Regards, Yang Ye ikedaike wrote: Hi I built GROMACS-3.3.3 with GCC-3.4.6 and OpenMPI-1.2.5 on CentOS 4.5(Intel Core2 Duo). I tested with gmxtest-3.3.3 and all tests passed in non-parallel. However, when I tested in parallel, I encountered the following messages. [Use 2 Cores] % ./gmxtest.pl -np 2 all Will test on 2 processors All 16 simple tests PASSED FAILED. Check files in dec+water 1 out of 14 complex tests FAILED All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file Can I ignore above messages about the pdb2gmx test? [Use 8 Cores] % ./gmxtest.pl -np 8 all Will test on 8 processors FAILED. Check files in angles1 FAILED. Check files in angles125 FAILED. Check files in bham FAILED. Check files in bonds1 FAILED. Check files in bonds125 FAILED. Check files in dih1 FAILED. Check files in dih125 FAILED. Check files in g96angles1 FAILED. Check files in g96angles125 FAILED. Check files in g96bonds1 FAILED. Check files in g96bonds125 FAILED. Check files in imp1 FAILED. Check files in imp36 FAILED. Check files in morse FAILED. Check files in rb1 FAILED. Check files in rb125 16 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in aminoacids FAILED. Check files in argon FAILED. Check files in butane FAILED. Check files in dec+water FAILED. Check files in ethyleenglycol No topol.tpr file in fe_test. grompp failed FAILED. Check files in fe_test FAILED. Check files in field FAILED. Check files in nacl FAILED. Check files in sw FAILED. Check files in tip4p FAILED. Check files in tip4pflex FAILED. Check files in urea FAILED. Check files in water 14 out of 14 complex tests FAILED FAILED. Check files in kernel010 FAILED. Check files in kernel020 FAILED. Check files in kernel030 FAILED. Check files in kernel100 FAILED. Check files in kernel101 FAILED. Check files in kernel102 FAILED. Check files in kernel103 FAILED. Check files in kernel104 FAILED. Check files in kernel110 FAILED. Check files in kernel111 FAILED. Check files in kernel112 FAILED. Check files in kernel113 FAILED. Check files in kernel114 FAILED. Check files in kernel120 FAILED. Check files in kernel121 FAILED. Check files in kernel122 FAILED. Check files in kernel123 FAILED. Check files in kernel124 FAILED. Check files in kernel130 FAILED. Check files in kernel131 FAILED. Check files in kernel132 FAILED. Check files in kernel133 FAILED. Check files in kernel134 FAILED. Check files in kernel200 FAILED. Check files in kernel201 FAILED. Check files in kernel202 FAILED. Check files in kernel203 FAILED. Check files in kernel204 FAILED. Check files in kernel210 FAILED. Check files in kernel211 FAILED. Check files in kernel212 FAILED. Check files in kernel213 FAILED. Check files in kernel214 FAILED. Check files in kernel220 FAILED. Check files in kernel221 FAILED. Check files in kernel222 FAILED. Check files in kernel223 FAILED. Check files in kernel224 FAILED. Check files in kernel230 FAILED. Check files in kernel231 FAILED. Check files in kernel232 FAILED. Check files in kernel233 FAILED. Check files in kernel234 FAILED. Check files in kernel300 FAILED. Check files in kernel301 FAILED. Check files in kernel302 FAILED. Check files in kernel303 FAILED. Check files in kernel304 FAILED. Check files in kernel310 FAILED. Check files in kernel311 FAILED. Check files in kernel312 FAILED. Check files in kernel313 FAILED. Check files in kernel314 FAILED. Check files in kernel320 FAILED. Check files in kernel321 FAILED. Check files in kernel322 FAILED. Check files in kernel323 FAILED. Check files in kernel324 FAILED. Check files in kernel330 FAILED. Check files in kernel331 FAILED. Check files in kernel332 FAILED. Check files in kernel333 FAILED. Check files in kernel334 63 out of 63 kernel tests FAILED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file I don't know why the all tests failed. Could you please give the information about test in parallel ? Thank you in advance. Teru ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [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 search the archive at http://www.gromacs.org/search before posting! Please don't post (un)sub
[gmx-users] nature of gromacs / gcc-4.x problem
Hello, I am trying to track down the exact nature of the gcc-4.1.x / gromacs bug. I have a system on which we were forced to reinstall gromacs (3.3.1 and 3.3.3) about 2 weeks ago and I didn't realize that the default gcc was bumped to 4.1.2. I am interested because ideally we won't need to throw out the last two weeks of simulation. The installation went fine and I have just run the tests in serial single precision, which all passed (except dec+water, although that was as indicated to be actually ok on the wiki... LJ (SR) step 34: -0.21167, step 34:-0.147217) I searched the archives, but a simple search for gcc is overwhelming and I couldn't find anything specific. I did find some references to the bugzilla (without links), but even when I search for gcc on bugzilla I get Zarro Boogs found. Thanks, Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Run test in parallel
Hi I built GROMACS-3.3.3 with GCC-3.4.6 and OpenMPI-1.2.5 on CentOS 4.5(Intel Core2 Duo). I tested with gmxtest-3.3.3 and all tests passed in non-parallel. However, when I tested in parallel, I encountered the following messages. [Use 2 Cores] % ./gmxtest.pl -np 2 all Will test on 2 processors All 16 simple tests PASSED FAILED. Check files in dec+water 1 out of 14 complex tests FAILED All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file Can I ignore above messages about the pdb2gmx test? [Use 8 Cores] % ./gmxtest.pl -np 8 all Will test on 8 processors FAILED. Check files in angles1 FAILED. Check files in angles125 FAILED. Check files in bham FAILED. Check files in bonds1 FAILED. Check files in bonds125 FAILED. Check files in dih1 FAILED. Check files in dih125 FAILED. Check files in g96angles1 FAILED. Check files in g96angles125 FAILED. Check files in g96bonds1 FAILED. Check files in g96bonds125 FAILED. Check files in imp1 FAILED. Check files in imp36 FAILED. Check files in morse FAILED. Check files in rb1 FAILED. Check files in rb125 16 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in aminoacids FAILED. Check files in argon FAILED. Check files in butane FAILED. Check files in dec+water FAILED. Check files in ethyleenglycol No topol.tpr file in fe_test. grompp failed FAILED. Check files in fe_test FAILED. Check files in field FAILED. Check files in nacl FAILED. Check files in sw FAILED. Check files in tip4p FAILED. Check files in tip4pflex FAILED. Check files in urea FAILED. Check files in water 14 out of 14 complex tests FAILED FAILED. Check files in kernel010 FAILED. Check files in kernel020 FAILED. Check files in kernel030 FAILED. Check files in kernel100 FAILED. Check files in kernel101 FAILED. Check files in kernel102 FAILED. Check files in kernel103 FAILED. Check files in kernel104 FAILED. Check files in kernel110 FAILED. Check files in kernel111 FAILED. Check files in kernel112 FAILED. Check files in kernel113 FAILED. Check files in kernel114 FAILED. Check files in kernel120 FAILED. Check files in kernel121 FAILED. Check files in kernel122 FAILED. Check files in kernel123 FAILED. Check files in kernel124 FAILED. Check files in kernel130 FAILED. Check files in kernel131 FAILED. Check files in kernel132 FAILED. Check files in kernel133 FAILED. Check files in kernel134 FAILED. Check files in kernel200 FAILED. Check files in kernel201 FAILED. Check files in kernel202 FAILED. Check files in kernel203 FAILED. Check files in kernel204 FAILED. Check files in kernel210 FAILED. Check files in kernel211 FAILED. Check files in kernel212 FAILED. Check files in kernel213 FAILED. Check files in kernel214 FAILED. Check files in kernel220 FAILED. Check files in kernel221 FAILED. Check files in kernel222 FAILED. Check files in kernel223 FAILED. Check files in kernel224 FAILED. Check files in kernel230 FAILED. Check files in kernel231 FAILED. Check files in kernel232 FAILED. Check files in kernel233 FAILED. Check files in kernel234 FAILED. Check files in kernel300 FAILED. Check files in kernel301 FAILED. Check files in kernel302 FAILED. Check files in kernel303 FAILED. Check files in kernel304 FAILED. Check files in kernel310 FAILED. Check files in kernel311 FAILED. Check files in kernel312 FAILED. Check files in kernel313 FAILED. Check files in kernel314 FAILED. Check files in kernel320 FAILED. Check files in kernel321 FAILED. Check files in kernel322 FAILED. Check files in kernel323 FAILED. Check files in kernel324 FAILED. Check files in kernel330 FAILED. Check files in kernel331 FAILED. Check files in kernel332 FAILED. Check files in kernel333 FAILED. Check files in kernel334 63 out of 63 kernel tests FAILED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file I don't know why the all tests failed. Could you please give the information about test in parallel ? Thank you in advance. Teru ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] remove center of mass motion
M. Emal Alekozai wrote: Dear All, I have a trajectory where the center of mass motion is not removed. In the mdrun.mdp file the option "comm-grps" was commented out: ; mode for center of mass motion removal = comm-mode= Linear ; number of steps for center of mass motion removal = nstcomm = 1 ; group(s) for center of mass motion removal = ;comm-grps= Protein SOL How can I remove the center of mass motion form a trajectory which was created with the above settings? I found an old posting [1] in the Gromacs mailinglist but no answer to it. 1: http://www.gromacs.org/pipermail/gmx-users/2006-November/024751.html You might find this thread more useful: http://www.gromacs.org/pipermail/gmx-users/2006-June/022169.html If you do a search for "center of mass trjconv" you will come up with lots of results that suggest using various iterations of trjconv -fit or trjconv -center. -Justin Thanks Emal -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromos function type assigned by grompp
Hi I am trying to set a calculation based on the GROMOS force field in a program I have and I am using GROMACS to generate the (starting) input files for me. From reading the manual I know that GROMOS uses a fourth power potential (type 2) for bonds and a cosine based angle potential (type 2), but I noticed that when using grompp to include the values for the parameters explicitly it changes the type from 2 to 1, for example: topology file before grompp [ bonds ] ; aiaj functc0c1c2c3 1 2 2gb_2 1 3 2gb_2 1 4 2gb_2 1 5 2gb_20 5 6 2gb_26 510 2gb_26 after using grompp [ bonds ] ; aiaj tp parameters NH1 1 0.1 1.87e+07 NH2 1 0.1 1.87e+07 NH3 1 0.1 1.87e+07 NCA 1 0.147 8.71e+06 CACB 1 0.153 7.15e+06 CA C 1 0.153 7.15e+06 Is this right? Also, for clarification, I know Gromacs uses kj/mol and nm as units, so does that mean that the values included in the ff*.itp files under the share/top/ directory are in those units? Also I noticed that the .itp files for bonding interactions in gmxbon.itp have declared a type 1 function which would be the regular harmonic one. Sorry for the very basic questions, but I wanted to be certain about this things, thanks!! Romelia Thanks! -- Romelia Salomon Miller Group 316 Noyes Chemistry Department Caltech ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] top file definitions_1
[EMAIL PROTECTED] wrote: Dear Community, I am trying to manually define a .top file of an organic molecule (a modified bisphosphonate). I am not a gromacs user but a lab mate is, so he will make the run. It has been several days since I started to search for a text where the .top format is depicted in detail but the only document I found was the one of the UREA molecule. (http://www.gromacs.org/component/option,com_wrapper/Itemid,165/). Just for future reference - when posting links, open the frame in a new window and post that URL. The one you post is the Search page, and not an actual post :) I need to have a detailed and didactic description of fields between [ ] and their columns of data just to understand the example of the UREA. Try reading Chapter 5 of the manual. By the way, do you know whether there is a forum to share parameters of molecules? Check the User Contributions section of the Gromacs site (within Downloads). -Justin Thank you very much, Best regards, Pablo Rosi. mail2web.com – What can On Demand Business Solutions do for you? http://link.mail2web.com/Business/SharePoint ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] top file definitions_1
Dear Community, I am trying to manually define a .top file of an organic molecule (a modified bisphosphonate). I am not a gromacs user but a lab mate is, so he will make the run. It has been several days since I started to search for a text where the .top format is depicted in detail but the only document I found was the one of the UREA molecule. (http://www.gromacs.org/component/option,com_wrapper/Itemid,165/). I need to have a detailed and didactic description of fields between [ ] and their columns of data just to understand the example of the UREA. By the way, do you know whether there is a forum to share parameters of molecules? Thank you very much, Best regards, Pablo Rosi. mail2web.com What can On Demand Business Solutions do for you? http://link.mail2web.com/Business/SharePoint ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] remove center of mass motion
Dear All, I have a trajectory where the center of mass motion is not removed. In the mdrun.mdp file the option "comm-grps" was commented out: ; mode for center of mass motion removal = comm-mode= Linear ; number of steps for center of mass motion removal = nstcomm = 1 ; group(s) for center of mass motion removal = ;comm-grps= Protein SOL How can I remove the center of mass motion form a trajectory which was created with the above settings? I found an old posting [1] in the Gromacs mailinglist but no answer to it. 1: http://www.gromacs.org/pipermail/gmx-users/2006-November/024751.html Thanks Emal -- Pt! Schon das coole Video vom GMX MultiMessenger gesehen? Der Eine für Alle: http://www.gmx.net/de/go/messenger03 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Determining temperature from velocities
I was wondering how g_energy determines the temperature of the groups. I am trying to measure temperature based upon distance from a point radially outward. To implement I thought about writing a code to input the final velocities to determine average temperature based upon a central point. Thanks, Andy ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] peptide translation
Dear All, I have a lipid - peptide system and while running the production run I forgot to assign comm-grps, thus the peptide has actually shifted from the center towards one of the edges. I have searched the forum and tried all possible options in trjconv i.e. -center zero, -fit translation, progressive etc. but mostly the entire bilayer shifts but the peptide does not move from its place. I am selecting the "Protein" option from trjconv when it asks for "group used for centering" How to translate the peptide only in a lipid-peptide system to a certain point? This is a short peptide in the top layer of the lipid bilayer and my bilayer center is at (0,0,0). I want to put the peptide at (0,0,1.7). I even tried using the shift option, but that does some weird things. Searching forum results in centering peptide in a water box i.e. peptide or protein at 0,0,0 and also mainly the threads that are already there talks about using trjconv center and translation options! I really apologize if I missed out any thread related to this and shall be really grateful if experts out there would kindly help me out. eagerly waiting for the response, Priyanka... Be the first one to try the new Messenger 9 Beta! Go to http://in.messenger.yahoo.com/win/___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] membrane with OPLS force field
Volker Wirth wrote: Hi Justin, thanks a lot for your response! Of course my mail was a bit "provocative", as I know that combination methods are state of the art, used in many publications and leading to reasonable results. (time scale eight months). Combining different force fields (Berger/GROMOS, Berger/OPLS) for lipids and proteins would be too complex, also setting up GAFF for another lipid system (DMPC, DMPS and I am curious to know what you believe to be "too complex" about the GROMOS/Berger and OPLS/Berger combinations. Certainly arguments can be made that combining force fields is questionable, but it's about the best we've got for now. Using GROMOS with Berger effectively requires simple addition What I had in mind was that combining different force fields (which represent different models of nature) increases the complexity of the simulation and we need to do more intensive tests on the results, to prove that we don't actually observe an effect of "interference" or something like that. There is this paper by Tieleman et al.: Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid–protein interactions, side chain transfer free energies and model proteins D Peter Tieleman et al 2006 J. Phys.: Condens. Matter 18 S1221-S1234 doi: 10.1088/0953-8984/18/28/S07 They point out that finding parameters for combined systems is a very delicate problem (it is possible, though) - so the idea to use one force field for the complete system looks much more inviting for me (and the paper of Shirley et al. presents very good results for their system with GAFF - _without_ protein, of course). OK, I'm not yet sure about the method I should use... Definitely a quandary I know many of us face. There isn't one perfect, self-consistent force field. Maybe one day :) Each has its limitations, and so far the combination method seems to be the most widely used. Up to you to do whatever you feel is the most justifiable. -Justin - Volker of parameters to the correct locations in .itp files, and while using OPLS does require a bit of work in making the correct conversions, it can be done in about 20 minutes if you use spreadsheet software. Just something to consider. Good reference; I recently came across it as well. -Justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Some Issues on Substrates/PBC
André Farias de Moura wrote: Hi Michael, if you are not interested in the substrate dynamics, then you could try the freeze group options (freezegrps and freezedim). I have used these options for graphite and it worked just fine. best, André In addition to that, you may consider using pbc = full to get an infinite system and potentially avoid some of those edge effects it looks like you are seeing. I know others have used that kind of setup with carbon nanotubes (not my area of expertise, but I've read the discussions). -Justin Dear Listmembers, This post is quite lengthy because it contains several different problems that I came across during my simulations and that I cannot figure out up to now. I included some links to pictures to give you some visualization and would be glad for every suggestion or hint even to part of my problems. Generally for my simulations I need substrates of silicon oxide and graphite (each one in different simulations). The substrate fills the simulation box completely in x-y direction so it should look like an infinite surface considering the periodic boundary conditions. The simulation with silicon oxide is working fine but I experienced some strange thing though: When the .gro file contains negative coordinates and I generate a .tpr for 4 nodes the structure is messed up totally after energy minimization (although it converges and gives no errors). I guess that the breaking up in four parts is somehow connected to the 4 nodes, because generating and running a 1 node .tpr solves this problem and the structure keeps intact after em - see pictures here: ( http://tinyurl.com/59zfda ). When I shift the coordinates in the .gro with editconf so that every coordinate is positive the structure can be em with both 1 or 4 node without problems. For the main md I have to stick with 1 node anyway because I get a "Shake block crossing node boundaries" error when I try to use 4 nodes. I found the advise to use less nodes in the mailing list archives and as I said it works for me, too, but is there any other way to get around this? For the test runs I'm doing now 1 node is fine, but for the real simulations later on I would like to use more nodes because the system will get bigger... With the graphite I have another problem: Again I have to stick with only one node, otherwise the structure is broken after energy minimization (with 4 nodes http://tinyurl.com/5eqngz ). Additionally here the energy minimization is not converging even after 2500 steps, forces keep in the range of 10^4 but I can still do a md with this file that is not exploding (md with the starting structure without any energy minimization will result in an exploding system as one might expect). After energy minimization the graphite sheets (four are in the simulation) are bended up/down correspondently to the connected periodic boundary at the edges of the simulation box (box is triclinic, http://tinyurl.com/5m72ke ). When I run an md with this as starting structure without position restraints on the carbon atoms, the sheets cleave beginning from the edges and then reunite in a curled conformation within 10ps ( http://tinyurl.com/5j4l3z ). If I put position restraints on all carbon atoms the graphite keeps flat, but of course I still have the up/down bending at the box edges, which I also want to get rid off to have a real "infinite" graphite surface. First I thought that this was maybe a problem of my graphite structure not fitting into my simulation box (hence the curling of the surface) but I checked the bonding lengths and b0 in the topology, the unit cell vectors and box vectors thoroughly and everything seems to be right. If I copy my simulation box and shift it by one of the box vectors I get a perfect continuation without any deviation on the boundaries, so everything seems like it should be for the starting structure. I also simulated the same graphite sheets within a bigger box, so that border carbons could not feel their counterparts over the periodic boundaries. That gave no distortion at the edges after em and the em converged, but of course in this way I cannot get an continous surface. Even stranger is, that after em the whole structure coordinates are shifted into the neighbouring periodic cell! For a bigger system with some additionally molecules that should absorb to the graphite surface the graphite sheets even ended up in different periodic images of the simulation box after em ( http://tinyurl.com/5uaxfa ). Maybe that's more a visualization problem because the following md simulation shows, that the molecules adsorb to the surface nevertheless (as one would suggest from pbc). Of course I can reconfigure my .gro for visualization by substracting or adding the box vectors untill all atoms end up inside the 'real' simulation box, but is it really supposed to behave that way, or is there something definitely wrong with my structure? I saw this "shifting" of the whole substrate into an
Re: [gmx-users] Some Issues on Substrates/PBC
Hi Michael, if you are not interested in the substrate dynamics, then you could try the freeze group options (freezegrps and freezedim). I have used these options for graphite and it worked just fine. best, André > Dear Listmembers, > > This post is quite lengthy because it contains several different problems > that > I came across during my simulations and that I cannot figure out up to > now. I > included some links to pictures to give you some visualization and would > be > glad for every suggestion or hint even to part of my problems. > > Generally for my simulations I need substrates of silicon oxide and > graphite > (each one in different simulations). The substrate fills the simulation > box > completely in x-y direction so it should look like an infinite surface > considering the periodic boundary conditions. > > The simulation with silicon oxide is working fine but I experienced some > strange thing though: When the .gro file contains negative coordinates and > I > generate a .tpr for 4 nodes the structure is messed up totally after > energy > minimization (although it converges and gives no errors). I guess that the > breaking up in four parts is somehow connected to the 4 nodes, because > generating and running a 1 node .tpr solves this problem and the structure > keeps intact after em - see pictures here: ( http://tinyurl.com/59zfda ). > When > I shift the coordinates in the .gro with editconf so that every coordinate > is > positive the structure can be em with both 1 or 4 node without problems. > > For the main md I have to stick with 1 node anyway because I get a "Shake > block crossing node boundaries" error when I try to use 4 nodes. I found > the > advise to use less nodes in the mailing list archives and as I said it > works > for me, too, but is there any other way to get around this? For the test > runs > I'm doing now 1 node is fine, but for the real simulations later on I > would > like to use more nodes because the system will get bigger... > > With the graphite I have another problem: Again I have to stick with only > one > node, otherwise the structure is broken after energy minimization (with 4 > nodes http://tinyurl.com/5eqngz ). Additionally here the energy > minimization > is not converging even after 2500 steps, forces keep in the range of 10^4 > but > I can still do a md with this file that is not exploding (md with the > starting > structure without any energy minimization will result in an exploding > system > as one might expect). After energy minimization the graphite sheets (four > are > in the simulation) are bended up/down correspondently to the connected > periodic boundary at the edges of the simulation box (box is triclinic, > http://tinyurl.com/5m72ke ). When I run an md with this as starting > structure > without position restraints on the carbon atoms, the sheets cleave > beginning > from the edges and then reunite in a curled conformation within 10ps ( > http://tinyurl.com/5j4l3z ). > > If I put position restraints on all carbon atoms the graphite keeps flat, > but > of course I still have the up/down bending at the box edges, which I also > want > to get rid off to have a real "infinite" graphite surface. > > First I thought that this was maybe a problem of my graphite structure not > fitting into my simulation box (hence the curling of the surface) but I > checked the bonding lengths and b0 in the topology, the unit cell vectors > and > box vectors thoroughly and everything seems to be right. If I copy my > simulation box and shift it by one of the box vectors I get a perfect > continuation without any deviation on the boundaries, so everything seems > like > it should be for the starting structure. > > I also simulated the same graphite sheets within a bigger box, so that > border > carbons could not feel their counterparts over the periodic boundaries. > That > gave no distortion at the edges after em and the em converged, but of > course > in this way I cannot get an continous surface. > > Even stranger is, that after em the whole structure coordinates are > shifted > into the neighbouring periodic cell! For a bigger system with some > additionally molecules that should absorb to the graphite surface the > graphite > sheets even ended up in different periodic images of the simulation box > after > em ( http://tinyurl.com/5uaxfa ). Maybe that's more a visualization > problem > because the following md simulation shows, that the molecules adsorb to > the > surface nevertheless (as one would suggest from pbc). Of course I can > reconfigure my .gro for visualization by substracting or adding the box > vectors untill all atoms end up inside the 'real' simulation box, but is > it > really supposed to behave that way, or is there something definitely wrong > with my structure? > > I saw this "shifting" of the whole substrate into another periodic image > of > the simulation box also in the simulation with the silicon substrate: it > 'jumped' into the periodic c
Re: [gmx-users] membrane with OPLS force field
Hi Justin, thanks a lot for your response! Of course my mail was a bit "provocative", as I know that combination methods are state of the art, used in many publications and leading to reasonable results. >> (time scale eight months). Combining different force fields >> (Berger/GROMOS, Berger/OPLS) for lipids and proteins would be too >> complex, also setting up GAFF for another lipid system (DMPC, DMPS and > I am curious to know what you believe to be "too complex" about the > GROMOS/Berger and OPLS/Berger combinations. Certainly arguments can be made > that combining force fields is questionable, but it's about the best we've > got for now. Using GROMOS with Berger effectively requires simple addition What I had in mind was that combining different force fields (which represent different models of nature) increases the complexity of the simulation and we need to do more intensive tests on the results, to prove that we don't actually observe an effect of "interference" or something like that. There is this paper by Tieleman et al.: Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid–protein interactions, side chain transfer free energies and model proteins D Peter Tieleman et al 2006 J. Phys.: Condens. Matter 18 S1221-S1234 doi: 10.1088/0953-8984/18/28/S07 They point out that finding parameters for combined systems is a very delicate problem (it is possible, though) - so the idea to use one force field for the complete system looks much more inviting for me (and the paper of Shirley et al. presents very good results for their system with GAFF - _without_ protein, of course). OK, I'm not yet sure about the method I should use... - Volker > of parameters to the correct locations in .itp files, and while using OPLS > does require a bit of work in making the correct conversions, it can be done > in about 20 minutes if you use spreadsheet software. > > Just something to consider. Good reference; I recently came across it as > well. > > -Justin > >> >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.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 [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > > > Justin A. Lemkul > Graduate Research Assistant > 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://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ### 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Some Issues on Substrates/PBC
Dear Listmembers, This post is quite lengthy because it contains several different problems that I came across during my simulations and that I cannot figure out up to now. I included some links to pictures to give you some visualization and would be glad for every suggestion or hint even to part of my problems. Generally for my simulations I need substrates of silicon oxide and graphite (each one in different simulations). The substrate fills the simulation box completely in x-y direction so it should look like an infinite surface considering the periodic boundary conditions. The simulation with silicon oxide is working fine but I experienced some strange thing though: When the .gro file contains negative coordinates and I generate a .tpr for 4 nodes the structure is messed up totally after energy minimization (although it converges and gives no errors). I guess that the breaking up in four parts is somehow connected to the 4 nodes, because generating and running a 1 node .tpr solves this problem and the structure keeps intact after em - see pictures here: ( http://tinyurl.com/59zfda ). When I shift the coordinates in the .gro with editconf so that every coordinate is positive the structure can be em with both 1 or 4 node without problems. For the main md I have to stick with 1 node anyway because I get a "Shake block crossing node boundaries" error when I try to use 4 nodes. I found the advise to use less nodes in the mailing list archives and as I said it works for me, too, but is there any other way to get around this? For the test runs I'm doing now 1 node is fine, but for the real simulations later on I would like to use more nodes because the system will get bigger... With the graphite I have another problem: Again I have to stick with only one node, otherwise the structure is broken after energy minimization (with 4 nodes http://tinyurl.com/5eqngz ). Additionally here the energy minimization is not converging even after 2500 steps, forces keep in the range of 10^4 but I can still do a md with this file that is not exploding (md with the starting structure without any energy minimization will result in an exploding system as one might expect). After energy minimization the graphite sheets (four are in the simulation) are bended up/down correspondently to the connected periodic boundary at the edges of the simulation box (box is triclinic, http://tinyurl.com/5m72ke ). When I run an md with this as starting structure without position restraints on the carbon atoms, the sheets cleave beginning from the edges and then reunite in a curled conformation within 10ps ( http://tinyurl.com/5j4l3z ). If I put position restraints on all carbon atoms the graphite keeps flat, but of course I still have the up/down bending at the box edges, which I also want to get rid off to have a real "infinite" graphite surface. First I thought that this was maybe a problem of my graphite structure not fitting into my simulation box (hence the curling of the surface) but I checked the bonding lengths and b0 in the topology, the unit cell vectors and box vectors thoroughly and everything seems to be right. If I copy my simulation box and shift it by one of the box vectors I get a perfect continuation without any deviation on the boundaries, so everything seems like it should be for the starting structure. I also simulated the same graphite sheets within a bigger box, so that border carbons could not feel their counterparts over the periodic boundaries. That gave no distortion at the edges after em and the em converged, but of course in this way I cannot get an continous surface. Even stranger is, that after em the whole structure coordinates are shifted into the neighbouring periodic cell! For a bigger system with some additionally molecules that should absorb to the graphite surface the graphite sheets even ended up in different periodic images of the simulation box after em ( http://tinyurl.com/5uaxfa ). Maybe that's more a visualization problem because the following md simulation shows, that the molecules adsorb to the surface nevertheless (as one would suggest from pbc). Of course I can reconfigure my .gro for visualization by substracting or adding the box vectors untill all atoms end up inside the 'real' simulation box, but is it really supposed to behave that way, or is there something definitely wrong with my structure? I saw this "shifting" of the whole substrate into another periodic image of the simulation box also in the simulation with the silicon substrate: it 'jumped' into the periodic cell and then jumped back one frame later. The other present (small) molecules stayed in the real simulation box all the time. I guess that this is maybe a problem caused by the substrate "molecule" filling up the whole simulation cell (at least in xy), but is there a way of getting Gromacs to always write out coordinates that lie within the real simulation cell instead of an periodic image? And is there a way of defining
Re: [gmx-users] membrane with OPLS force field
Volker Wirth wrote: standard acyl chain parameters fail when they get too long. I think there ref. for that is a Berendsen paper on hexadecane simulations, but I could be wrong there. In any event, 'protein' parameters do not appear to transfer directly to long acyl chains in a simple way and therefore your non-coulombic parameters may also need to be parameterized. I understand your motivation to do this, and of course your parameters would be widely accepted if they produced good bulk properties, but we're talking about an entire phd project here, so I suggest that you don't plan to have this up and running from scratch in the next few months. As I read more about membrane simulation, I found this interesting article: Shirley W. I. Siu, Robert Vácha, Pavel Jungwirth, and Rainer A. Böckmann Biomolecular simulations of membranes: Physical properties from different force fields J. Chem. Phys. 128, 125103 (2008); DOI:10.1063/1.2897760 They compare GAFF, Berger and Charmm27 simulating a DOPC system with experimental results. The best ff seems to be GAFF (Generalized Amber FF, all atom), but there is no 'super' force field for _both_ membrane and protein. I am looking for a straightforward method to use in my diploma thesis (time scale eight months). Combining different force fields (Berger/GROMOS, Berger/OPLS) for lipids and proteins would be too complex, also setting up GAFF for another lipid system (DMPC, DMPS and mixed bilayers) won't be possible and in the moment the idea is to use the paper's approach to get at least a simulation with **PC lipids. I am curious to know what you believe to be "too complex" about the GROMOS/Berger and OPLS/Berger combinations. Certainly arguments can be made that combining force fields is questionable, but it's about the best we've got for now. Using GROMOS with Berger effectively requires simple addition of parameters to the correct locations in .itp files, and while using OPLS does require a bit of work in making the correct conversions, it can be done in about 20 minutes if you use spreadsheet software. Just something to consider. Good reference; I recently came across it as well. -Justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE[4]: Define proper set of topology parameters for new molecule in different FF.
>>I want to construct TOPOLOGY of many different molecules using different >>Force Fields (FF). >> >>If i want to describe , for example, METHYL ACETATE in OPLS-AA force field >> >> O Hc5 >> || | >> C---O1C2Hc4 >> | | >>Hc3-- C1--Hc2 Hc6 >> | >> Hc1 >>1) I'll find all ATOM TYPES in oplsaa, let`s imagine that they are like >>in the image above. >>2) then i describe all BONDS and PAIRS >>3) then i should define BOND ANGLES >> but how much angles should i describe? >> PRODRG and topologies in share/top give all possible angles, >> but is there overestimation of FF energy in such cases, as: >> angle O-C-C1 >> angle O-C-O1 >> angle O1-C-C1 >> 3 adjoining angles in planar group? >>4) then i should define PROPER and IMPROPER DIHEDRALS. >> Should i define all possible DIHEDRALS as it is made in GMX >>share/top/urea.itp? >> Or should i define only those DIHEDRALS that are exist in chosen FF? >> Are there any rules how to chose these parameters? >> >>For the first view it seems that you should chose these parameters like >>they were parametrized in chosen FF. >> => the "topology graph" (gmx topology without all FF values) is > >>different for different FF? > >> Am i right? > >> And in order to describe the molecular TOPOLOGY in CERTAIN FF we > >>should know the special "rules" for THIS FF, > >>=> mail to author of FF or read initial papers. > >> Am i right? > >> > >>The initial papers do not contain CLEAR description of how to chose > >>proper set of parameters. > >> I`m interested in GROMOS, OPLS-UA, OPLS-AA, AMBER-UA, AMBER-AA FF, > >>MMFF94. > >> So, if you know any rules or useful links i'll be very thankful. > >>I`m very sorry if my questions are mentioned already, but i did not find > >>the answer in mailing-list. > >>Kindest regards, > >You should describe the values of those parameters you want either >constrain or simulate with intramolecular parameters. Evidently, you >need a set of values completely determining the geometry of your >molecule. However, you make want some atom groups to rotate during the >simulation, then you need not to give the respective numbers. >For an example just see the existing FF provided with GROMACS.. >Dear Dr. Chaban, > >Thanks a lot for your reply. >I`m very sorry but it seems that you did not properly >understand the goal of the letter. >1) The aim is to create a topology in certain FF >that`s why we should follow the methodology of parametrization of this FF (to >my mind). >|=> the "topology graph" (gmx topology without all FF values) is not FF independent. > Am i right? >2) To describe exact 3D structure of molecule we should > define 2*N-5 angles (bond angles or/and dihedrals) (N-number of atoms), > besides of all bonds. >(that`s my empirical formula). > In gmx provided topologies there is no possibility to understand > what is the final topology of residue (RTP file: there are only bonds > and improper dihedrals, what about others: bond angles, and proper > dihedral?) > > share/top/urea.itp: there are all possible bond angles > H8 proper dihedrals (max value) > |3 improper dihedral (max value) > N--H > | >O=C--N--H >| >H >The set of parameters is more then enough. > > share/top/benzamide.itp: (that is not realy benzamide if we`ll see > WIKIpedia) >Hthere are set of parameters that is greater that it >| should be to define 3D structure, but less then the max > value. >N--H > __ | >/O \_C--N--H >\__/| > H > >Again the questions are the same as in the first letter. > >Thanks a lot. >I`m looking forward to your reply. >Andrey Frolov. If you have found all the atom types you need in the OPLSAA try to use 'x2top' in order to generate a topology for a certain compound from your PDB(or xyz?) structure. It seems to be the quickest way for your persue. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to fix the center of mass of the protein in the pull simulation
Dear users: how to fix the center of mass of the protein in the pull simulation? I want to know to know! Please help me! - 雅虎邮箱，您的终生邮箱！___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: how to fix the COM of group in the pull.
>Dear users: >I want to know how to fix the com of the group in the pull or afm simulation,Please give some ideas. comm-grps in grompp.mdp, isn't it? -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] membrane with OPLS force field
> standard acyl chain parameters fail when they get too long. I think there > ref. for that is a Berendsen paper on hexadecane simulations, but I could be > wrong there. In any event, 'protein' parameters do not appear to > transfer directly to long acyl chains in a simple way and therefore your > non-coulombic parameters may also need to be parameterized. > > I understand your motivation to do this, and of course your parameters would > be widely accepted if they produced > good bulk properties, but we're talking about an entire phd project here, so > I suggest that you don't plan to > have this up and running from scratch in the next few months. > As I read more about membrane simulation, I found this interesting article: Shirley W. I. Siu, Robert Vácha, Pavel Jungwirth, and Rainer A. Böckmann Biomolecular simulations of membranes: Physical properties from different force fields J. Chem. Phys. 128, 125103 (2008); DOI:10.1063/1.2897760 They compare GAFF, Berger and Charmm27 simulating a DOPC system with experimental results. The best ff seems to be GAFF (Generalized Amber FF, all atom), but there is no 'super' force field for _both_ membrane and protein. I am looking for a straightforward method to use in my diploma thesis (time scale eight months). Combining different force fields (Berger/GROMOS, Berger/OPLS) for lipids and proteins would be too complex, also setting up GAFF for another lipid system (DMPC, DMPS and mixed bilayers) won't be possible and in the moment the idea is to use the paper's approach to get at least a simulation with **PC lipids. -- ### Volker Wirth Center for Medical Physics and Technology Biophysics Group FAU Erlangen-Nuremberg Email: vwirth%at%biomed.uni-erlangen.de ### (lɯʇɥ˙dılɟ/ɯoɔ˙pɐɟʌǝɹ˙ʍʍʍ//:dʇʇɥ) ¡ʇuǝɹǝɟɟıp ʞuıɥʇ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] A fix to eigio.c ?
make_edi crashes on 3.3.3 (but not on 3.3.1). I think the problem is in eigio.c where the following lines were added after 3.3.1: eignr=NULL; eigval=NULL; eigvec=NULL; I guess it should be: *eignr=NULL; *eigval=NULL; *eigvec=NULL; Elad P. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
