[gmx-users] error compiling mopac and gromacs
Hi I am trying to link mopac with gromacs in a 32 bit linux machine. I have downloaded the libmopac.a file and kept it under /usr/local/lib. I installed fftw with double precision and then I set the enviornmental variables for linking mopac and gromacs export LDFLAGS=-L/usr/local/lib -Wl,--wrap,__ctype_b export CPPFLAGS=/usr/local/include -DUSE_MOPAC export LIBS=lmopac then I have ran the ./configure --with-qmmm-mopac --disable-float.It seems to run ok.Then I used the make command but an error is comming as follows- /usr/local/lib/libmopac.a(lread.o)(.text+0x160): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x21f): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x296): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x2d0): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x8b2): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0xb05): more undefined references to `__wrap___ctype_b' follow collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/usr/gromacs-4.0.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/usr/gromacs-4.0.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/usr/gromacs-4.0.3/src' make: *** [all-recursive] Error 1 Please suggest where I have gone wrong. Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: GROMACS on CYGWIN
I was wondering whether GROMACS on CYGWIN is less capable than GROMACS run on LINUX? i.e. concerning its speed and its ability to simulate larger macromolecules. I assume that it is faster, but is it very much different? I would be very grateful for your help. There are no considerable differences between gromacs on CYGWIN and LINUX, to my knowledge. If you are interested in running gromacs on WINDOWS-desktop, I would also suggest to look at the systems based on http://www.colinux.org/ kernel . My broad experience with them shows they are very powerful to run both gromacs and (manifold) visualizarion utitilies. Good luck. Dr. Vitaly Chaban -- 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: Subject: [gmx-users] error compiling mopac and gromacs
Depending on how your libmopac.a was biuld, you need the to include the f2c or g2c library as well. Gerrit Message: 5 Date: Sat, 12 Jun 2010 14:33:02 +0530 (IST) From: subarna thakur thakur.suba...@yahoo.co.in Subject: [gmx-users] error compiling mopac and gromacs To: gmx-users@gromacs.org Message-ID: 371899.78968...@web95516.mail.in.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hi I am trying to link mopac with gromacs in a 32 bit linux machine. I have downloaded the libmopac.a file and kept it under /usr/local/lib. I installed fftw with double precision and then I set the enviornmental variables for linking mopac and gromacs export LDFLAGS=-L/usr/local/lib -Wl,--wrap,__ctype_b export CPPFLAGS=/usr/local/include -DUSE_MOPAC export LIBS=lmopac then I have ran the ./configure --with-qmmm-mopac --disable-float.It seems to run ok.Then I used the make command but an error is comming as follows- /usr/local/lib/libmopac.a(lread.o)(.text+0x160): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x21f): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x296): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x2d0): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x8b2): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0xb05): more undefined references to `__wrap___ctype_b' follow collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/usr/gromacs-4.0.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/usr/gromacs-4.0.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/usr/gromacs-4.0.3/src' make: *** [all-recursive] Error 1 Please suggest where I have gone wrong. Subarna Thakur -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100612/ed0e12b1/attachment.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 74, Issue 69 * -- Gerrit Groenhof MPI biophysical chemistry Goettingen Germany http://wwwuser.gwdg.de/~ggroenh/ -- 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] Selecting specific atoms to find average energy of
On Jun 12, 2010, at 3:10 AM, Justin A. Lemkul wrote: Quoting Jennifer Casey jrcase...@gmail.com: Hello, I ran an md simulation, and I have graphed the total average energy of the system by using g_energy to convert my binary .edr file into a text based file. What I want to do is to find the average energy between the solvent molecules, excluding the energy between the solute-solvent molecules and the solute-solute molecules. I was unable to find a way to have g_energy give me the energy between a specific group. Is it possible to do this? Or do I need to rerun the simulation, and include something like energy monitor groups? There is probably a simple command for this that I am missing (or at least I hope there is). I would prefer not to have to rerun all of my md simulations. You will have to rerun your simulations using a new .tpr file with the desired energygrps defined. The good news is that you simply have to rerun the trajectory using mdrun -rerun, which is substantially faster than recalculating the whole thing from scratch. Some complement: - you have to rerun the trr trajectory file to access hight precision coordinates of your system. - you'll have to change the update the neighbor list every step (nstlist=1). If not your energies won't be accurate. -Justin Thanks in advance, Jennifer Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] restraints in one direction
Hi, Is it not possible to use gromacs restraints only in one direction, e.g. X can be less than A (const) with no penalty force, but if XA then the force appears trying to X-A ? Maybe some artifial tricks are possible to achieve that? -- Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: parameters of Sodium Sulfate
Hmm... What's the problem? OPLS contains the parameters both for S and O. If you want a better model of this anion, I'd suggest to look for the respective articles. Also, if I'm not mistaken [(SO4)2-] topology was present somewhere in the original gromacs distribution. Best. Dr. Vitaly Chaban On Sat, Jun 12, 2010 at 4:03 PM, shiva birgani sh.birg...@gmail.com wrote: Hi I am trying to simulate Lysozyme in solution of water and Sodium Sulfate (Na2SO4). But I don’t know how I can look for the parameters of [(SO4)2-] in OPLS -Force field. Could you please help me in this regards? regards Shiva Birgani -- 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] write topology by hand
Hi everyone, I had a .pdb file that was drug_enzyme complex. Drug was GOL(Glycerol) and I wrote topology file by hand but now when I run grompp command I have this error:Fatal error:Syntax error - File ffoplsaabon.itp, line 4Last line read:'[ bondtypes ]'Invalid order for directive bondtypes and I don't know how can I do this? Thank you _ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969-- 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] write topology by hand
Quoting you zou zou@live.com: Hi everyone, I had a .pdb file that was drug_enzyme complex. Drug was GOL(Glycerol) and I wrote topology file by hand but now when I run grompp command I have this error:Fatal error:Syntax error - File ffoplsaabon.itp, line 4Last line read:'[ bondtypes ]'Invalid order for directive bondtypes and I don't know how can I do this? Have you consulted the manual for required topology format? How about the Gromacs website? You probably would have found this: http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_defaults If you need specific advice, you'll need to provide the relevant snippets of the topology (including the problematic line). -Justin Thank you _ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969 Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: parameters of Sodium Sulfate
What about sulfonate, does anyone has parameters for [(SO3)-] On Sat, Jun 12, 2010 at 9:17 AM, Vitaly Chaban vvcha...@gmail.com wrote: Hmm... What's the problem? OPLS contains the parameters both for S and O. If you want a better model of this anion, I'd suggest to look for the respective articles. Also, if I'm not mistaken [(SO4)2-] topology was present somewhere in the original gromacs distribution. Best. Dr. Vitaly Chaban On Sat, Jun 12, 2010 at 4:03 PM, shiva birgani sh.birg...@gmail.com wrote: Hi I am trying to simulate Lysozyme in solution of water and Sodium Sulfate (Na2SO4). But I don’t know how I can look for the parameters of [(SO4)2-] in OPLS -Force field. Could you please help me in this regards? regards Shiva Birgani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: parameters of Sodium Sulfate
It is better for you to search the literature on simulation sulfonate. The general purpose FFs are not oriented towards the inorganic ions. Anyway, you will need good charge distributions for these ions. I am sure that the aqueous solutions of sulphates have been already simulated by means of classical MD. Maybe, even in 1990x. Dr. Vitaly Chaban On Sat, Jun 12, 2010 at 8:35 PM, fang yuan fangyuan3...@gmail.com wrote: What about sulfonate, does anyone has parameters for [(SO3)-] On Sat, Jun 12, 2010 at 9:17 AM, Vitaly Chaban vvcha...@gmail.com wrote: Hmm... What's the problem? OPLS contains the parameters both for S and O. If you want a better model of this anion, I'd suggest to look for the respective articles. Also, if I'm not mistaken [(SO4)2-] topology was present somewhere in the original gromacs distribution. Best. Dr. Vitaly Chaban On Sat, Jun 12, 2010 at 4:03 PM, shiva birgani sh.birg...@gmail.com wrote: Hi I am trying to simulate Lysozyme in solution of water and Sodium Sulfate (Na2SO4). But I don’t know how I can look for the parameters of [(SO4)2-] in OPLS -Force field. Could you please help me in this regards? regards Shiva Birgani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: write topology by hand
Hi everyone, I had a .pdb file that was drug_enzyme complex. Drug was GOL(Glycerol) and I wrote topology file by hand but now when I run grompp command I have this error:Fatal error:Syntax error - File ffoplsaabon.itp, line 4Last line read:'[ bondtypes ]'Invalid order for directive bondtypes and I don't know how can I do this? Thank you I suppose you have too many $include in your topol.top. Normally if everything was done by hand, you do not need [bondtypes] but only [bonds] to run grompp successfully. Note, this is true if you have the complete entries (!) (with constants) for bonds, angles, etc in your topology. Good luck. Dr. Vitaly Chaban -- 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] Andersen thermostat
Hi, I want to use the Andersen Thermostat (not v-rescale). But I get an error when I try to use it. My mdp file is as below: title=NPT simulation for a 2D WCA system cpp =/lib/cpp ; RUN CONTROL PARAMETERS integrator = md dt = 0.0005 nsteps = 400 ; OUTPUT CONTROL OPTIONS nstxout = 50 ; No output, except for last frame (coordinates) nstvout = 0; No output, except for last frame (velocities) nstfout = 0; No output, except for last frame (forces) nstlog = 100 ; Write every nth step to the log nstenergy= 100 ; Write energies at every n step nstxtcout= 0 ; Do not write a compressed tr ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Cut-off rcoulomb = 1.1225 vdw-type = Cut-off rvdw = 1.1225 ; Temperature coupling tcoupl = Andersen tc-grps = ARAR tau_t= 0.1 ref_t= 120.2717 andersen_seed=-1 ; Pressure coupling pcoupl = Berendsen pcoupltype = semiisotropic tau-p= 0.20 0.20 compressibility = 1e-5 0 ;Dont know ref-p= 50 0 ;Generate velocities for startup run gen_vel =yes gen_temp =120.2717 gen_seed =-1 ;Constraints constraints = all-bonds constraint_algorithm= LINCS lincs_order = 4 lincs_iter = 1 lincs_warnangle = 90 ;unconstrained_start= no ;shake_tol = 0.0001 Any idea why this would not work? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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
