[gmx-users] Use the TIP4P water model in the gmx2 force field
Hello, I want to use the tip4p water model in the gmx2 force field, but it seems that it doesn't have the nobond parameter of the OWT4 in the gmx2 force field ,does it need add by myself? look forward to your respond. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] install problem of ngmx.
Hello, I installed the gromacs4.0.5, when I made, it had lots of mistakes, below is some of the mistakes: In file included from ngmx.c:50: Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory Xstuff.h:51:28: error: X11/cursorfont.h: No such file or directory Xstuff.h:52:27: error: X11/Xresource.h: No such file or directory In file included from ./xutil.h:43, from ./xdlgitem.h:42, from xdlg.h:40, from dialogs.h:40, from ngmx.c:54: ./x11.h:57: error: expected specifier-qualifier-list before 'Display' ./x11.h:79: error: expected declaration specifiers or '...' before 'XEvent' ./x11.h:79: error: expected declaration specifiers or '...' before 'Window' ./x11.h:82: error: expected specifier-qualifier-list before 'Window' In file included from ./xdlgitem.h:42, from xdlg.h:40, from dialogs.h:40, from ngmx.c:54: ./xutil.h:49: error: expected specifier-qualifier-list before 'Window' ./xutil.h:57: error: expected ')' before 'win' ./xutil.h:61: error: expected ')' before '*' token ./xutil.h:63: error: expected declaration specifiers or '...' before 'XFontStruct' ./xutil.h:63: error: expected declaration specifiers or '...' before 'Drawable' ./xutil.h:67: error: expected declaration specifiers or '...' before 'Drawable' ./xutil.h:75: error: expected ')' before '*' token ./xutil.h:77: error: expected ')' before '*' token ./xutil.h:79: error: expected ')' before '*' token ./xutil.h:81: error: expected ')' before '*' token ./xutil.h:84: error: expected ')' before '*' token ./xutil.h:87: error: expected ')' before '*' token ./xutil.h:89: error: expected ')' before '*' token ./xutil.h:91: error: expected ')' before '*' token In file included from xdlg.h:40, from dialogs.h:40, from ngmx.c:54: ./xdlgitem.h:66: error: expected specifier-qualifier-list before 'Pixmap' ./xdlgitem.h:98: error: expected declaration specifiers or '...' before 'XEvent' ./xdlgitem.h:142: error: expected declaration specifiers or '...' before 'Pixmap' In file included from dialogs.h:40, from ngmx.c:54: xdlg.h:63: error: expected specifier-qualifier-list before 'Window' xdlg.h:81: error: expected declaration specifiers or '...' before 'Window' xdlg.h:140: error: expected declaration specifiers or '...' before 'Window' In file included from pulldown.h:40, from dialogs.h:41, from ngmx.c:54: popup.h:44: error: expected specifier-qualifier-list before 'Window' popup.h:53: error: expected specifier-qualifier-list before 'Window' popup.h:58: error: expected specifier-qualifier-list before 'Window' popup.h:64: error: expected declaration specifiers or '...' before 'Window' In file included from dialogs.h:41, from ngmx.c:54: pulldown.h:51: error: expected declaration specifiers or '...' before 'Window' In file included from manager.h:45, from dialogs.h:42, from ngmx.c:54: nleg.h:54: error: expected declaration specifiers or '...' before 'Window' In file included from manager.h:46, from dialogs.h:42, from ngmx.c:54: buttons.h:64: error: expected declaration specifiers or '...' before 'Window' buttons.h:64: error: expected declaration specifiers or '...' before 'Window' buttons.h:69: error: expected declaration specifiers or '...' before 'Window' buttons.h:69: error: expected declaration specifiers or '...' before 'Window' In file included from dialogs.h:42, from ngmx.c:54: manager.h:133: error: expected declaration specifiers or '...' before 'Window' In file included from dialogs.h:43, from ngmx.c:54: logo.h:44: error: expected specifier-qualifier-list before 'XFontStruct' logo.h:53: error: expected declaration specifiers or '...' before 'Window' In file included from ngmx.c:57: nmol.h:43: error: expected declaration specifiers or '...' before 'Window' ngmx.c:65: error: expected declaration specifiers or '...' before 'Window' ngmx.c: In function 'dump_xw': ngmx.c:70: error: 'w' undeclared (first use in this function) ngmx.c:70: error: (Each undeclared identifier is reported only once ngmx.c:70: error: for each function it appears in.) ngmx.c:411: error: 't_x11' has no member named 'bg' ngmx.c:412: warning: passing argument 7 of 'init_pd' makes pointer from integer without a cast ngmx.c:412: warning: passing argument 8 of 'init_pd' from incompatible pointer type ngmx.c:412: warning: passing argument 9 of 'init_pd' from incompatible pointer type ngmx.c:412: error: too many arguments to function 'init_pd' make[3]: *** [ngmx.o] Error 1 make[3]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src/ngmx' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src' make: *** [all-recursive] Error 1 I hope you can give me some suggestions to solve the problom。 Thank you very much!-- 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! Plea
[gmx-users] hou to Construct the oil/water interface
Hello, I want to construct the oil/water interface, like this: X and Y axises of the box are 5 nm, Z axis is 10 nm. 0-5 nm of Z axis in the box is water, and 5-10 nm of Z axis in the box is oil (for example :dodecane), how can I achieve the aim? Thank you very much! -- 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] How to deal with the top files
Hello，I have one box,which has two kinds of solvents and two kinds of solutes. How can I put the infermation of them in one top fles, or what shall I do to Setup the energy minimization, for the infermation is not in the same top file ? Thank you ! -- 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] isntall problem of ngmx
Hello, I have done the ./configure --without-X,why it still would compile the ngmx? I had posted to you that it would make errores if compiled the ngmx. the errores are like this : In file included from ngmx.c:50: Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory Xstuff.h:51:28: error: X11/cursorfont.h: No such file or directory Xstuff.h:52:27: error: X11/Xresource.h: No such file or directory In file included from ./xutil.h:43, from ./xdlgitem.h:42, from xdlg.h:40, from dialogs.h:40, from ngmx.c:54: ./x11.h:57: error: expected specifier-qualifier-list before 'Display' ./x11.h:79: error: expected declaration specifiers or '...' before 'XEvent' ./x11.h:79: error: expected declaration specifiers or '...' before 'Window' ./x11.h:82: error: expected specifier-qualifier-list before 'Window' In file included from ./xdlgitem.h:42, from xdlg.h:40, from dialogs.h:40, from ngmx.c:54: ngmx.c:412: warning: passing argument 7 of 'init_pd' makes pointer from integer without a cast ngmx.c:412: warning: passing argument 8 of 'init_pd' from incompatible pointer type ngmx.c:412: warning: passing argument 9 of 'init_pd' from incompatible pointer type ngmx.c:412: error: too many arguments to function 'init_pd' make[3]: *** [ngmx.o] Error 1 make[3]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src/ngmx' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/mnt/soft/chemtec/gromacs-4.0.5/src' make: *** [all-recursive] Error 1 Thank you !-- 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] install problem of ngmx
Hello, my configure line is ./configure --without-X --enable-mpi --enable-fortran --prefix=/mnt/soft/chemtec/gromacs4.0.5. I have been setted in the ~/.bashrc like this : export PATH=/opt/mpich2wgs/bin:$PATH:/share/apps/intel/fce/10.1.022/bin export CC=gcc export CXX=g++ export CFLAGS="-03 xport CXXFLAGS="-03 " export FFLAGS="-03 " export CPPFLAGS=-I/mnt/soft/chemtec/fftw3.2.1/include export LDFLAGS=-L/ mnt/soft/chemtec/fftw3.2.1/lib export F77=ifort export LD_LIBRARY_PATH=/opt/mpich2wgs/lib/:$LD_LIBRARY_PATH the version of the gcc is 4.1.1. Thank you!-- 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] install problem of ngmx
Hello, the error is like that : *In file included from ngmx.c:50:* > > *Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory* > > *Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory* > > *Xstuff.h:51:28: error: X11/cursorfont.h: No such file or directory* > > *Xstuff.h:52:27: error: X11/Xresource.h: No such file or directory* > but in my system, it has the Xlib.h,Xutil.h,cursorfont.h,Xresource.h in the /usr/X11R6/include /X11 file. Where I should put these documents in can it finds?-- 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] How to change the resname?
Hello, first, I make a grateful acknowledgement for Mark and Justin's help to guide me to install the gromacs,I have installed it well. I have another question need you help , could I change the resname in the .gro and .top or .itp documents? if yes, how shall I do, just change it ? Thank you !-- 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] How to set the density of the box?
Hello, I want to set the density of the box (e.g. set 1 g/ml for the water box). I use the density option in the editconf, then use the genbox to generate the box, but the result of the density is not what I setted. How can I do ? I have another question, I don't find the tip3p.gro and spce.gro water model in the top file, only have the .itp document. if I want to generate the TIP3P water box, how can I do, or where can I get the tip3p.gro and spce.gro documents? Thank you !-- 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] TIP3P water box
Hello,I want to use spc216.gro and apply the tip3p.itp parameters, but it would make a mistake for the pre-processor "grompp" ,it said can't find HW atomtypes, the force file which I used is "ffG43a1.itp". my tip3p.itp file is as follows: [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; id at type res nr residu name at name cg nr charge #ifdef _FF_OPLS 1 opls_111 1 SOL OW 1 -0.834 2 opls_112 1 SOL HW1 1 0.417 3 opls_112 1 SOL HW2 1 0.417 #endif #ifdef _FF_CHARMM 1 OT 1 SOL OW 1 -0.834 2 HT 1 SOL HW1 1 0.417 3 HT 1 SOL HW2 1 0.417 #endif #ifdef _FF_GROMACS 1 OWT3 1 SOL OW 1 -0.834 2 HW 1 SOL HW1 1 0.417 3 HW 1 SOL HW2 1 0.417 #endif #ifdef _FF_GROMOS96 1 OWT3 1 SOL OW 1 -0.834 2 HW 1 SOL HW1 1 0.417 3 HW 1 SOL HW2 1 0.417 #endif #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572 502416.0 1 3 1 0.09572 502416.0 0.09572 502416.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 #else [ settles ] ; i j funct length 1 1 0.09572 0.15139 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif the version of the gromacs is 4.0.5. Thank you for all 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] How to use the walls
Hello, I had posted this message yesterday,maybe it was missing.I want to use the wall for 2d periodic boundary, but I don't know how to set the wall_type and wall_density, I don't know what thay depend on for setting. I also want to know the format of them for setting. Thank you !-- 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] warning when process the files with grompp
Hello, I want to generate the em.tpr file, but it arise the warning like this : Warning: atom name 1 in TBP_wat.top and 10tbpc12wat1.gro does not match (C13 - OW) Warning: atom name 2 in TBP_wat.top and 10tbpc12wat1.gro does not match (C10 - HW1) Warning: atom name 3 in TBP_wat.top and 10tbpc12wat1.gro does not match (C7 - HW2) Warning: atom name 4 in TBP_wat.top and 10tbpc12wat1.gro does not match (C6 - OW) Warning: atom name 5 in TBP_wat.top and 10tbpc12wat1.gro does not match (O5 - HW1) Warning: atom name 6 in TBP_wat.top and 10tbpc12wat1.gro does not match (P1 - HW2) Warning: atom name 7 in TBP_wat.top and 10tbpc12wat1.gro does not match (O4 - OW) My system is water and dodecane (from 0 to 5 nm of the z axis is water box, 5 to 10 nm dodecane box), and the TBP dissolves in the dodecane, if I overlook it , mdrun can not do the energy minimization well, and the TBP molecule will be tattered. I hope you can help me ,thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the error for 2D periodic boundary
Hello, when I use the 2D periodic boundary for the pr run , it just ran several steps then exited, the log file has some error message like this : Program mdrun, VERSION 4.0.5 Source code file: nsgrid.c, line: 357 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 -1. It should have been within [ 0 .. 432 ] If I use the 3D periodic boundary, it would be OK, but I have to use the 2D periodic boundary for my simulation, I don't know what is the reason. my pr.mdp file is below: title = 10tbppr cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 3 ; total 60.0 ps. nstcomm = 1 nstxout = 100 nstvout = 100 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 5 ns_type = grid rlist = 1.0 ; Eledtrostatics coulombtype = PME rcoulomb = 1.0 ;distance for the coulomb cut-off ; VdW vdwtype = cut-off rvdw = 1.4 DispCorr = EnerPres ;Ewald fourierspacing = 0.3 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3dc optimize_fft = yes ;Pbc and walls pbc = xy ;ns_type must be grid nwall = 2 wall_type = 10-4 wall_atomtype = SI SI wall_density = 10 10 wall_r_linpot = 0.5 ; Berendsen temperature coupling is on in three groups Tcoupl = v-rescale tau_t = 0.1 0.1 0.1 tc_grps = SOL C12 TBP ref_t = 300 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman pcoupltype = semiisotropic tau_p = 0.5 compressibility = 0 4.5e-5 ref_p = 1.0 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 could you help me analyze the reason? thank you very much !-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the problem of the periodic boundary
Hello, I use the 2D periodic boundary along the x and y axises, it has a strange thing. my solvent is dodecane, I view the output trajectory in the VMD, for one molecule, it has some part in the left(top), and some in the right(bottom), it still connections to each other, how to solve this problem? Thank you !-- 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] calculate interfacial tension
Hello, I want to calculate the interfacial tension of the oil/water interface . I use 2D periodic boundary along Z axis , I get the interfacial teision from the .edr file (namely #Surf*SurfTen), it seems that the Surf*SurfTen is the total tension of the two interface ,is it that ? Does it has any influence for I use the 2D periodic boundary along Z axis ? Waiting for your reply eagerly. Thank you ! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the broken of the molecules
Hello, I do the energy minimization of the butylene box , but some butylene molecules are broken after that. The butylene itp file is produced by PRODRG, as follows: [ moleculetype ] ; Name nrexcl BUT 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 BUT C9 1 0.0049 15.0350 2 CH2 1 BUT C6 1 -0.02442 14.0270 3 C 1 BUT C3 1 0.07957 13.0190 4 C 1 BUT C2 1 -0.06005 14.0270 [ bonds ] ; ai aj fu c0, c1, ... 2 1 2 0.155 715.0 0.155 715.0 ; C6 C9 2 3 2 0.153 715.0 0.153 715.0 ; C6 C3 3 4 2 0.135 715.0 0.135 715.0 ; C3 C2 [ pairs ] ; ai aj fu c0, c1, ... 1 4 1 ; C9 C2 [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2 112.5 520.0 112.5 520.0 ; C9 C6 C3 2 3 4 2 125.0 610.0 125.0 610.0 ; C6 C3 C2 [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 1 2 3 4 1 0.0 1.0 6 0.0 1.0 6 ; dih C9 C6 C3 C2 Can you show me why the butylene molecules would be broken? Thank you very much ! -- 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
