Re: [gmx-users] compiling problem
Is LAM-MPI's binary in PATH? if you run mpicc from console, will it also show No such file or directory? Check LAM-MPI installation. Regards, Yang Ye On Wed, Sep 16, 2009 at 12:39 PM, Mu Yuguang (Dr) y...@ntu.edu.sg wrote: Hi, I use git clone git://git.gromacs.org/gromacs.git to get the lastest version and ./bootstrap To generate the configure file Then use ./configure successfully Howeve, after make The error appears as foloowing: mpicc -DHAVE_CONFIG_H -I. -I. -I../../../../src -I/usr/X11R6/include -I/usr/include/libxml2 -I../../../../include -DGMXLIBDIR=\/home/ygmu/software/gmx_cvs/gromacs/share/top\ -I/home/ygmu/software/fftw-3.2/float/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -MT nb_kernel400_x86_64_sse.lo -MD -MP -MF .deps/nb_kernel400_x86_64_sse.Tpo -c nb_kernel400_x86_64_sse.c -o nb_kernel400_x86_64_sse.o nb_kernel400_x86_64_sse.c: In function `nb_kernel400_x86_64_sse': nb_kernel400_x86_64_sse.c:93: warning: implicit declaration of function `_mm_castsi128_ps' nb_kernel400_x86_64_sse.c:93: error: invalid initializer nb_kernel400_x86_64_sse.c:94: error: invalid initializer nb_kernel400_x86_64_sse.c:95: error: invalid initializer mpicc: No such file or directory make[5]: *** [nb_kernel400_x86_64_sse.lo] Error 1 Regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards, Yang Ye ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] compiling problem
Yang Ye wrote: Is LAM-MPI's binary in PATH? if you run mpicc from console, will it also show No such file or directory? Check LAM-MPI installation. Does 4.0.5 compile under the same conditions as the failure below? Mark On Wed, Sep 16, 2009 at 12:39 PM, Mu Yuguang (Dr) y...@ntu.edu.sg wrote: Hi, I use git clone git://git.gromacs.org/gromacs.git to get the lastest version and ./bootstrap To generate the configure file Then use ./configure successfully Howeve, after make The error appears as foloowing: mpicc -DHAVE_CONFIG_H -I. -I. -I../../../../src -I/usr/X11R6/include -I/usr/include/libxml2 -I../../../../include -DGMXLIBDIR=\/home/ygmu/software/gmx_cvs/gromacs/share/top\ -I/home/ygmu/software/fftw-3.2/float/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -MT nb_kernel400_x86_64_sse.lo -MD -MP -MF .deps/nb_kernel400_x86_64_sse.Tpo -c nb_kernel400_x86_64_sse.c -o nb_kernel400_x86_64_sse.o nb_kernel400_x86_64_sse.c: In function `nb_kernel400_x86_64_sse': nb_kernel400_x86_64_sse.c:93: warning: implicit declaration of function `_mm_castsi128_ps' nb_kernel400_x86_64_sse.c:93: error: invalid initializer nb_kernel400_x86_64_sse.c:94: error: invalid initializer nb_kernel400_x86_64_sse.c:95: error: invalid initializer mpicc: No such file or directory make[5]: *** [nb_kernel400_x86_64_sse.lo] Error 1 Regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Large fluctuation of protein temperature with nose hoover thermostat
Hi gromacs experts, For my simulations of peptide (8 AA) in water (5100, SPC/E) and with 1 Cl- i use the Nose-Hoover Thermostat to simulate in NVT ensemble. Since i am a beginner with GROMACS, i have a question with the tau_t parameters Parameters i used I ; Temperature coupling is on tcoupl = nose-hoover ; nose-hoover thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.4 0.4 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K When i compute temperature (15, 40 and 41) of the system with g_energy for 30 ns, i obtain the following values. Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 310 2.46886 2.46886 6.12135e-07 0.0171398 T-Protein 310 32.1134 32.1117 -4.10352e-05 -1.14898 T-Non-Protein 310 2.47549 2.47548 8.55869e-07 0.0239643 Heat Capacity Cv: 12.473 J/mol K (factor = 6.34265e-05) gcq#109: Ease Myself Into the Body Bag (P.J. Harvey) As you can see the temp fluctuation is larger ( 10 %) than the values for system and the solvent It is normal for you ? If not how to correct it Thank in advance for your help ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] some questions about the tabulated interaction functions
Dear GMXers, by looking through the manual, I find that the tabluated interaction functions seem very flexible for performing MD simulations. But some questions puzzle me too much: for bonded interactions, as for bonds, angles, dihedrals, the f'(x) are the derivations of f(x) respective to x, here x can be considered as values of bonds, angles, and dihedrals? for non-bonded interactions, as for coulomb and LJ, the f'(x) are the derivations of f(x) respective to x, here x can be considered as values of distance between non-bonded atoms? Thanks a lot for any reply to this post Sincerely, Chaofu Wu, Dr. _ 心跳斗地主新版体验，给你360度的心跳体验！ http://club.msn.cn/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] compiling problem
No, even I do not use mpi , the error is still there. Regards Yuguang From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yang Ye Sent: Wednesday, September 16, 2009 2:34 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] compiling problem Is LAM-MPI's binary in PATH? if you run mpicc from console, will it also show No such file or directory? Check LAM-MPI installation. Regards, Yang Ye On Wed, Sep 16, 2009 at 12:39 PM, Mu Yuguang (Dr) y...@ntu.edu.sgmailto:y...@ntu.edu.sg wrote: Hi, I use git clone git://git.gromacs.org/gromacs.githttp://git.gromacs.org/gromacs.git to get the lastest version and ./bootstrap To generate the configure file Then use ./configure successfully Howeve, after make The error appears as foloowing: mpicc -DHAVE_CONFIG_H -I. -I. -I../../../../src -I/usr/X11R6/include -I/usr/include/libxml2 -I../../../../include -DGMXLIBDIR=\/home/ygmu/software/gmx_cvs/gromacs/share/top\ -I/home/ygmu/software/fftw-3.2/float/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -MT nb_kernel400_x86_64_sse.lo -MD -MP -MF .deps/nb_kernel400_x86_64_sse.Tpo -c nb_kernel400_x86_64_sse.c -o nb_kernel400_x86_64_sse.o nb_kernel400_x86_64_sse.c: In function `nb_kernel400_x86_64_sse': nb_kernel400_x86_64_sse.c:93: warning: implicit declaration of function `_mm_castsi128_ps' nb_kernel400_x86_64_sse.c:93: error: invalid initializer nb_kernel400_x86_64_sse.c:94: error: invalid initializer nb_kernel400_x86_64_sse.c:95: error: invalid initializer mpicc: No such file or directory make[5]: *** [nb_kernel400_x86_64_sse.lo] Error 1 Regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Regards, Yang Ye ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
