[gmx-users] problem with angle restraints
I trying to use angle restrain for an ligand molecule. I have included the following information in my .itp file of the ligand - [ angle_restraints ] ; aiajak functc0c1c2c3 6 1 7 1 106.9510001 6 1 8 1 108.8310001 7 1 8 1 104.9610001 5 2 7 1 110.6610001 5 2 8 1 104.9810001 When I am running the grompp command , I am getting an error- Incorrect number of parameters - found 2, expected 3 or 6 for Angle Rest.. -- I have gone through the manual it says that for angle restrains we have to provide the theta(degree);fc; multi.I have given all the relevant information but still there is error. Please tell me 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
Re: [gmx-users] Frozen N2 in a very long tube
- Original Message - From: shuai shuai bansh...@gmail.com Date: Saturday, July 10, 2010 2:27 Subject: [gmx-users] Frozen N2 in a very long tube To: gmx-users@gromacs.org Hear all, Recently I met a strong error from gromacs. Therefore I would like to know whether you have experienced the same thing or what is the reason for that. The system I simulated is nvt MD for N2 (with partial charge) How do you have partial charges on such a molecule? diffusion in a long tube (100x2.5x2.5 nm^3) at 300k. I get molecules freezed in a small cluster after a few ns. The weird thing is that I do not have such problem for either longer domain or short domain. The input parameters are: I'm afraid I don't understand what you mean by freezed in a small cluster, or a longer or shorter domain. Mark title= CNT ; Preprocessor - specify a full path if necessary. cpp = /lib/cpp include = define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 1000 ; For exact run continuation or redoing part of a run init_step= 0 ; 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= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd- fric = 0 ld- seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 10 nstvout = 10 nstfout = 10 ; Checkpointing helps you continue after crashes nstcheckpoint= 10 ; Output frequency for energies to log file and energy file nstlog = 10 nstenergy= 10 ; Output frequency and precision for xtc file nstxtcout= 1 xtc- precision= 100 ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb- switch = 0 rcoulomb = 1.0 ; Relative dielectric constant for the medium and the reaction field epsilon- r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw- type = Cut-off ; cut-off lengths rvdw- switch = 0 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table- extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = nose-hoover ; Groups to couple separately tc- grps = System ; Time constant (ps) and reference temperature (K) tau_t= 1 ref_t= 303.15 ; Pressure coupling Pcoupl = no Pcoupltype
[gmx-users] Re: the Pressure control in GROMACS 4.0.7
Dear users, I think the pressure control in gromacs 4.0.7 may have some problems. First ,The pressure value fluctuates widely ,even between -7984.377930 and 5920.053711 bar.Second,the average pressure sometimes is much larger than what I have set,for example, I have set ref_p = 1.0 , but the average is actually over 7 bar. It is because I have not set properly , or something else? Zhongjin He Hello Zhongjin: The average pressure in gromacs is really somewhat larger, e.g. if you request ref_p=1bar, you always get something close to P=1.3 bar. If somebody can comment on this issue, it will be interesting. Anyway, I think that the coupling in general is correct, since the simulated densities are as they are expected. As I suppose, the main reason is that pressure is not a nanoscopic property whereas your MD system is nanosized. I would advice you to gradually enlarge the system and monitor the pressure. It should give you some answers anyway. The average of 7 bar if one requests 1 bar, is weird. Look at the simulation time and the system size firstly. Best. -- Dr. Vitaly Chaban Associate Researcher -- 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: Frozen N2 in a very long tube
Dear Shuai: Please try to couple temperature for nanotube and nitrogen separately. BTW, what is your partial charge and how did you construct it? Good luck! Dr. Vitaly Chaban Recently I met a strong error from gromacs. Therefore I would like to know whether you have experienced the same thing or what is the reason for that. The system I simulated is nvt MD for N2 (with partial charge) diffusion in a long tube (100x2.5x2.5 nm^3) at 300k. I get molecules freezed in a small cluster after a few ns. The weird thing is that I do not have such problem for either longer domain or short domain. The input parameters are: -- 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: the Pressure control in GROMACS 4.0.7
On 2010-07-10 09.47, Vitaly Chaban wrote: Dear users, I think the pressure control in gromacs 4.0.7 may have some problems. First ,The pressure valuefluctuates widely ,even between -7984.377930 and 5920.053711 bar.Second,the average pressuresometimes is much larger than what I have set,for example, I have set ref_p = 1.0 , but the average isactually over 7 bar. It is because I have not set properly , or something else? Zhongjin He Hello Zhongjin: The average pressure in gromacs is really somewhat larger, e.g. if you request ref_p=1bar, you always get something close to P=1.3 bar. If somebody can comment on this issue, it will be interesting. Anyway, I think that the coupling in general is correct, since the simulated densities are as they are expected. fluctuations are proportional to 1/sqrt(natoms). The numbers Zhongjin mentions are extreme, for a 216 water box *in equilibrium* you would get 1 +/- 500-600 bar. I suspect your sytem may be out of equilibrium or very small. Whether the average is 1 or 5 does not make a difference if the fluctuation are two orders of magnitude larger. As I suppose, the main reason is that pressure is not a nanoscopic property whereas your MD system is nanosized. I would advice you to gradually enlarge the system and monitor the pressure. It should give you some answers anyway. The average of 7 bar if one requests 1 bar, is weird. Look at the simulation time and the system size firstly. Best. -- Dr. Vitaly Chaban Associate Researcher -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Installing gromacs from git
Hi, if you configure the git version without the --enable-mpi flag, it will turn on threads by default. Depending on the number of processors you have on your workstation, it will then use these many threads. You can disable that with mdrun -nt 1 ... Carsten On Jul 10, 2010, at 1:57 AM, Sai Pooja wrote: Hi, I had used the following steps to install a git version of gromacs. It installed correctly and I have been using it for a while. However, even though I didnt install the parallel version, when I use mdrun it runs in parallel. Is installation in the parallel mode by default? Is there a way to use it without parallelization? 301 cd gromacs 302 ls 303 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 304 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 305 clear 306 ls 307 ./configure --help 308 ./configure --prefix=/fs/home/sm868/gromacsnew 309 make log 310 ls 311 jmacs log 312 grep error log 313 grep Error log 314 make install Pooja On Sun, Jun 20, 2010 at 2:17 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: For future reference, I was able to install gromacs and this is what finally worked - installing gromacs in a folder different than the untared. It somehow helped to not create the folder but just directly using the name in the prefix 301 cd gromacs 302 ls 303 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 304 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 305 clear 306 ls 307 ./configure --help 308 ./configure --prefix=/fs/home/sm868/gromacsnew 309 make log 310 ls 311 jmacs log 312 grep error log 313 grep Error log 314 make install I got the msg - GROMACS is installed under /fs/home/sm868/gromacsnew. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Thanks for the help. *One question - There is already another version of gromacs installed in the /usr/local so I used a different directory to install it. Now do I need to use make links?* Do you normally make links? If so, you'll be over-writing the executables in /usr/local/bin. One other possible side effect is that if both /usr/local/bin and /usr/local/gromacs/bin are in your $PATH, you can't define which executable to use unambiguously without specifying the whole path name for each executable. If you're using several version of Gromacs concurrently on the same machine, it's probably best to just install them in their own locations and source the proper GMXRC when you log in to use the version you want. -Justin * * Pooja On Sun, Jun 20, 2010 at 2:17 AM, Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com wrote: I redid the entire thing after that first mail in which i reported the error related to fftw(including running the make uninstall commands and removing the folders entirely and getting fresh ones). I apologize for not specifying this and like I said... there seemed to be no errors this time except when I ran make install for gromacs. The error looks like this: make[3]: *** [install-man1] Error 1 make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/fs/home/sm868/gromacs/man' make: *** [install-recursive] Error 1 I didn't find any other error.. is there a way to look for them other than looking at what is being printed while the command is running? I tried $ grep Error */* in the folder but found nothing more than entries in different scripts etc. On Sun, Jun 20, 2010 at 1:27 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com Date: Sunday, June 20, 2010 15:09 Subject: Re: [gmx-users] Installing gromacs from git To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org History log: 189 ./configure --enable-threads --enable-float --prefix=/fs/home/sm868/fftw-3.2.2 190 make 191 clear 192 make install 193 cd .. 194 cd gromacs 195 ls 196 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 197 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 198 ./bootstrap 199 ls 200 ./configure --prefix=/fs/home/sm868/gromacs 201 make 202 make install Everything works till I get the following error with make install(after it runs for a while) :
[gmx-users] Re: Pressure control in GROMACS 4.0.7
Dear Professor van der Spoel: Don't you have an idea why the average value of pressure appears to be (always?) slightly larger and (never?) smaller than requested one? I did not collect the statistics systematically but I often mentioned this curious fact. Vitaly fluctuations are proportional to 1/sqrt(natoms). The numbers Zhongjin mentions are extreme, for a 216 water box *in equilibrium* you would get 1 +/- 500-600 bar. I suspect your sytem may be out of equilibrium or very small. Whether the average is 1 or 5 does not make a difference if the fluctuation are two orders of magnitude larger. -- 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: Pressure control in GROMACS 4.0.7
On 2010-07-10 12.40, Vitaly Chaban wrote: Dear Professor van der Spoel: Don't you have an idea why the average value of pressure appears to be (always?) slightly larger and (never?) smaller than requested one? I did not collect the statistics systematically but I often mentioned this curious fact. My guess is that it is just coincidence. In fact I published a table of pressures with standard deviation in JCP 108 (1998) p. 10220 where some pressures are rounded to 0, most to 1 and some larger than 1. This is also my source for the fluctuations of 600 bar for a 216 molecule box. These were with RF and Cut-off, it might be slightly different for PME. Vitaly fluctuations are proportional to 1/sqrt(natoms). The numbers Zhongjin mentions are extreme, for a 216 water box *in equilibrium* you would get 1 +/- 500-600 bar. I suspect your sytem may be out of equilibrium or very small. Whether the average is 1 or 5 does not make a difference if the fluctuation are two orders of magnitude larger. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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: the Pressure control in GROMACS 4.0.7
Dear users: I am simulating a CNT in water. In the energy minimization step, I restrain the CNT by a constant 10e8,because I don't want the CNT to deform. After minimization,the energy is -44054.835938. Then NVT and NPT equilibration , at this step,the end C atoms are fixed by a constant 30 to prevent from being swept away. The temperature is OK. But the pressure may be not so proper.It is larger than the set value.It is OK? Energy Average RMSD Fluct. Drift Tot-Drift --- Pressure (bar) 1.5674 6891.48 6891.42 -0.100337 -100.337 the npt.mdp title = OPLS Lysozyme NPT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 50 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = yes ; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = CNT SOL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off pressure 0.00 -777.187622 0.20 4527.866211 0.40 -7984.377930 0.60 5585.704102 0.80 2807.166992 1.00 -3545.817383 1.20 4112.207031 1.40 2340.378906 1.60 -5803.378906 1.80 8399.341797 2.00 622.575745 2.20 -3483.511963 2.40 5920.053711 2.60 -1108.013306 2.80 -4201.218750 3.00 5663.891602 3.20 -4298.212402 3.40 -1245.458862 . 996.400024 -2921.789062 996.600037 3155.833008 996.800049 2046.963623 997.61 -3057.696045 997.200073 2390.562500 997.400024 3122.586182 997.600037 -254.417053 997.800049 -741.921631 998.61 -1757.483154 998.200073 -1241.035278 998.400024 15.855911 998.600037 316.152985 998.800049 1165.281250 999.61 1776.868286 999.200073 55.826385 999.400024 538.847107 999.600037 4052.162842 999.800049 -6294.055664 1000.61 -1811.536377 Thanks! Zhongjin He -- 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: the Pressure control in GROMACS 4.0.7
On 2010-07-10 15.56, zhongjin wrote: Dear users: I am simulating a CNT in water. In the energy minimization step, I restrain the CNT by a constant 10e8,because I don't want the CNT to deform. After minimization,the energy is -44054.835938. Then NVT and NPT equilibration , at this step,the end C atoms are fixed by a constant 30 to prevent from being swept away. The temperature is OK. But the pressure may be not so proper.It is larger than the set value.It is OK? Energy Average RMSD Fluct. Drift Tot-Drift Your position restraint force constant is so high that it will induce large fluctuations unless you use very short time steps. What happens if you turn the position restraints off? Or if you set the force constant to 1000 kJ/mol nm^2? Normally the CNT should not deform even without position restraints, but you might need to use improper dihedrals with the right parameters (which I don't know, check the literature). --- Pressure (bar) 1.5674 6891.48 6891.42 -0.100337 -100.337 the npt.mdp title = OPLS Lysozyme NPT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 50 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = yes ; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = CNT SOL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off pressure 0.00 -777.187622 0.20 4527.866211 0.40 -7984.377930 0.60 5585.704102 0.80 2807.166992 1.00 -3545.817383 1.20 4112.207031 1.40 2340.378906 1.60 -5803.378906 1.80 8399.341797 2.00 622.575745 2.20 -3483.511963 2.40 5920.053711 2.60 -1108.013306 2.80 -4201.218750 3.00 5663.891602 3.20 -4298.212402 3.40 -1245.458862 . 996.400024 -2921.789062 996.600037 3155.833008 996.800049 2046.963623 997.61 -3057.696045 997.200073 2390.562500 997.400024 3122.586182 997.600037 -254.417053 997.800049 -741.921631 998.61 -1757.483154 998.200073 -1241.035278 998.400024 15.855911 998.600037 316.152985 998.800049 1165.281250 999.61 1776.868286 999.200073 55.826385 999.400024 538.847107 999.600037 4052.162842 999.800049 -6294.055664 1000.61 -1811.536377 Thanks! Zhongjin He -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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: Frozen N2 in a very long tube
Dear all, thanks for your suggestions. During this NVT simulation, I keep nanotube rigid. So the temperature should only couple to Nitrogen instead of the whole system as my original input file. I will try to couple temperature only to nitrogen to see whether this is the reason. Many thanks again, especially Dr. Vitaly Chaban. shuai 2010/7/10 Vitaly Chaban vvcha...@gmail.com: Dear Shuai: Please try to couple temperature for nanotube and nitrogen separately. BTW, what is your partial charge and how did you construct it? Good luck! Dr. Vitaly Chaban Recently I met a strong error from gromacs. Therefore I would like to know whether you have experienced the same thing or what is the reason for that. The system I simulated is nvt MD for N2 (with partial charge) diffusion in a long tube (100x2.5x2.5 nm^3) at 300k. I get molecules freezed in a small cluster after a few ns. The weird thing is that I do not have such problem for either longer domain or short domain. The input parameters are: -- gmx-users mailing list gmx-us...@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] pdb2gmx with DNA
Hi Thanks, I thought so too. My command line is: pdb2gmx -f xxx.pdb file The -ter flag is set to default, i.e. charged termini. When I use the -ter flag for interactive termini selection and I select NONE for both N- and C-ter the message becomes: Program pdb2gmx, VERSION 4.0.99-dev-2010-07-07 08:35:28 -0700-7cbc3b9-dirty Source code file: pdb2top.c, line: 887 Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. For more information and tips for troubleshooting, please check the GROMACS Best George From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, July 09, 2010 8:08 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] pdb2gmx with DNA Patargias, George wrote: Thanks for your reply Justin. I am trying to generate a topology dor a dna structure using the charmm dna.rtp I have renamed the residue name to DA , DG etc. I have also set DA5 and DC3 for the 5' and 3' ends I got this error Fatal error: atom N not found in buiding block 2DG while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I quess I need to change something in the .rtp and/or the .tdb files. But what? Maybe, maybe not. It looks like pdb2gmx is trying to treat your DNA as protein. What is your command line? What are you choosing for termini? -Justin Thanks a lot George-- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://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: Frozen N2 in a very long tube
shuai shuai wrote: Dear all, thanks for your suggestions. During this NVT simulation, I keep nanotube rigid. So the temperature should only couple to Nitrogen instead of the whole system as my original input file. I will try to couple temperature only to nitrogen to see whether this is the reason. Many thanks again, especially Dr. Vitaly Chaban. This is not what has been suggested to you, nor does it sound terribly realistic. How can one element of a system be controlled by a thermostat, and the other not? If these two species interact (i.e. experience collisions), then it seems to me that they need to exchange energy in some way. Note, too, that now two people have asked you about your charges on N2. It seems like an odd physical model. In the future, you would benefit from posting this information, as well as a complete .mdp file for what you're doing. -Justin shuai 2010/7/10 Vitaly Chaban vvcha...@gmail.com: Dear Shuai: Please try to couple temperature for nanotube and nitrogen separately. BTW, what is your partial charge and how did you construct it? Good luck! Dr. Vitaly Chaban Recently I met a strong error from gromacs. Therefore I would like to know whether you have experienced the same thing or what is the reason for that. The system I simulated is nvt MD for N2 (with partial charge) diffusion in a long tube (100x2.5x2.5 nm^3) at 300k. I get molecules freezed in a small cluster after a few ns. The weird thing is that I do not have such problem for either longer domain or short domain. The input parameters are: -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://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] pdb2gmx with DNA
I think there have been changes to the way pdb2gmx handles termini, perhaps related to the impending inclusion of the ffamber ports, but I do not know. I worked with someone else with this issue, and it was solved by renaming residues, which seems like a terrible solution. I guess your DNA is being interpreted as protein, which certainly isn't correct. I would suggest filing a bugzilla for this; in theory, pdb2gmx should handle DNA and protein seamlessly, but something seems to be mishandled here. -Justin Patargias, George wrote: Hi Thanks, I thought so too. My command line is: pdb2gmx -f xxx.pdb file The -ter flag is set to default, i.e. charged termini. When I use the -ter flag for interactive termini selection and I select NONE for both N- and C-ter the message becomes: Program pdb2gmx, VERSION 4.0.99-dev-2010-07-07 08:35:28 -0700-7cbc3b9-dirty Source code file: pdb2top.c, line: 887 Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. For more information and tips for troubleshooting, please check the GROMACS Best George From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, July 09, 2010 8:08 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] pdb2gmx with DNA Patargias, George wrote: Thanks for your reply Justin. I am trying to generate a topology dor a dna structure using the charmm dna.rtp I have renamed the residue name to DA , DG etc. I have also set DA5 and DC3 for the 5' and 3' ends I got this error Fatal error: atom N not found in buiding block 2DG while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I quess I need to change something in the .rtp and/or the .tdb files. But what? Maybe, maybe not. It looks like pdb2gmx is trying to treat your DNA as protein. What is your command line? What are you choosing for termini? -Justin Thanks a lot George-- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://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] Treating nonbondend interactions in GROMACS
Hello Justin, Thanks for your comments and also I really liked your reasoning for getting no answer from people that are not awake : You are right ;) Actually, I have no charged particles in my system. All I have is carbon and hydrogen. I read through the manual meticulously about nonbonded interaction terms. I would like you to correct me if I am wrong. See the summary below (my understanding) please: Treating nonbonded interactions for a hydrocarbon system: 1-Short range: vdw: shift electrostatics: shift so the settings would be : rvdw=1 rcoulomb=1 rlist=1.1 rcoulomb-switch=0 (when this is zero means shift function is added to actual function for all r?) I have a question here: in manual I read setting this last parameter nonzero means it acts as a switch function. I thought if it is nonzero shift acts just at a nonzero-r between zero and r_c (rcoulomb or rvdw) 2-Long range vdw: Dispcorr:Enerpres electrostatics: PME There are 2 issues from last post (quotes) I am unsure about. in md.mdp file I have only coulombtype=PME This contradicts your statement above. You said you had only uncharged particles, but clearly this is not the case. What you mean is Basically that I dont need to consider PME for hydrocarbon system? and if you mean I am using wrong setting: I do not know how else I can treat LR electrostatics in my system. I read in the manual that PME almost for all cases performs better than Ewald and also PPPM cant do P coupling so I picked PME :) Also you said: A method like PME is significantly more accurate, but you can also achieve reasonable results using switch, shift, etc. Read about the relevant mechanics of the force field you're using for what might be appropriate. From what your statement above I realize that PME and shift or switch func's are different alternatives. To be honest I am a little confused about the methods for treating nonbonded interactions. Thats why I wrote that little summary above so that you can correct me. This could be useful for other beginners as well. My understanding from reading the manual is that PME is for LR and switch and shift functions for SR. How could they be alternatives? Thank you, On 9 July 2010 20:15, Justin A. Lemkul jalem...@vt.edu wrote: jojo J wrote: Dear experts, I posted this message before but I think you did not see it since I noticed messages after this have been replied. I have a hydrocarbon Messages do not receive replies in any sort of order. Probably no one has had any relevant comments yet, or they live in a time zone where they are not awake :) system with no charged particles. Today In one of the GROMACS tutorials I saw the following setting in em.mdp file: fourierspacing = 0.12 ;fourier_nx = 0 ;fourier_ny = 0 ;fourier_nz = 0 ;pme_order = 4 ;ewald_rtol = 1e-5 ;optimize_fft = yes has been used for PME . Sofar I did not even include coulombtype=PME in my em.mdp file. What I had was: constraints = all-bonds integrator = steep dt = 0.002; ps ! nsteps = 200 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; ; Energy minimizing stuff ; emtol = 1000.0 Can you please guide me whether it is necessary to include these lines in em file for system having only partial charges like hydrocarbon (alkane). Also, in md.mdp file I have only coulombtype=PME and not the This contradicts your statement above. You said you had only uncharged particles, but clearly this is not the case. above Ewald settings. Do you recommend to include those settings? For energy minimization, the effects of plain cutoffs may or may not be significant. Using plain cutoffs for actual simulation is a bad idea. The artifacts are well-documented and for modern simulations any good reviewer should raise an immediate concern if plain cutoffs were used and not thoroughly justified. A method like PME is significantly more accurate, but you can also achieve reasonable results using switch, shift, etc. Read about the relevant mechanics of the force field you're using for what might be appropriate. Without the mentioned lines I am getting reasonabel results (potential energy, kinetic, ,, also T coupling works perfectly). If I had better to unclude them what is the best value for fourierspacing? I don't think there's ever been any sort of systematic study on the effects of Fourier grid spacing. The trade-off is between speed and accuracy. Larger values speed up calculations, but make PME less accurate. Smaller values have the opposite effect. You could do a small test for yourself (0.12, 0.16, 0.18...) to see if there are any adverse effects. -Justin Thank you, -- Justin A. Lemkul Ph.D. Candidate ICTAS
Re: [gmx-users] Treating nonbondend interactions in GROMACS
jojo J wrote: Hello Justin, Thanks for your comments and also I really liked your reasoning for getting no answer from people that are not awake : You are right ;) Actually, I have no charged particles in my system. All I have is carbon and hydrogen. I read through the manual meticulously about nonbonded I have yet to see a force field that treats even hydrocarbon groups (like amino acid side chains) as completely uncharged. There is a slight electronegativity imbalance between C and H, so the bonds are slightly polar, even if the molecule, overall, is nonpolar. It is up to you to justify your model. Depending on how you treat your system may make the following points entirely irrelevant. If you indeed have 0 charge on all the atoms in your system, how you treat electrostatics is unimportant - there are no electrostatic interactions in your system at all. interaction terms. I would like you to correct me if I am wrong. See the summary below (my understanding) please: Treating nonbonded interactions for a hydrocarbon system: 1-Short range: vdw: shift electrostatics: shift so the settings would be : rvdw=1 rcoulomb=1 rlist=1.1 rcoulomb-switch=0 (when this is zero means shift function is added to actual function for all r?) Yes, you're shifting over the entire range of 0-1.1 nm. I have a question here: in manual I read setting this last parameter nonzero means it acts as a switch function. I thought if it is nonzero shift acts just at a nonzero-r between zero and r_c (rcoulomb or rvdw) No idea, sorry. 2-Long range vdw: Dispcorr:Enerpres electrostatics: PME There are 2 issues from last post (quotes) I am unsure about. in md.mdp file I have only coulombtype=PME This contradicts your statement above. You said you had only uncharged particles, but clearly this is not the case. What you mean is Basically that I dont need to consider PME for hydrocarbon system? Or any method for electrostatics at all. and if you mean I am using wrong setting: I do not know how else I can treat LR electrostatics in my system. I read in the manual that PME almost for all cases performs better than Ewald and also PPPM cant do P coupling so I picked PME :) Also you said: A method like PME is significantly more accurate, but you can also achieve reasonable results using switch, shift, etc. Read about the relevant mechanics of the force field you're using for what might be appropriate. From what your statement above I realize that PME and shift or switch func's are different alternatives. To be honest I am a little confused about the methods for treating nonbonded interactions. Thats why I wrote that little summary above so that you can correct me. This could be useful for other beginners as well. My understanding from reading the manual is that PME is for LR and switch and shift functions for SR. How could they be alternatives? You don't pick a separate short-range and long-range method for either vdW or Coulombic interactions. Dispersion correction is applied for systems using plain vdW cutoffs to account for truncation artifacts. There are several basic textbooks that discuss this. For PME, the short-range interactions are treated by a modified switch function. See the manual, section 4.1.6 for the description. The remaining electrostatics (beyond rcoulomb) are calculated in reciprocal space. So by setting coulombtype = PME you treat short-range and long-range effects simultaneously. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://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
