[gmx-users] Re: FCC lattice of argon
Ahmed - This is *YOUR* research, not mine. I believe I have given you enough hints to succeed. Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA On Fri, May 25, 2012 at 12:51 PM, ahmed sta wrote: > Can you help me please > > > Thanks for all > > ____ > De : Dr. Vitaly V. Chaban > À : ahmed sta > Cc : gmx-users@gromacs.org > Envoyé le : Vendredi 25 mai 2012 17h33 > Objet : Re: Re : Re : Re : Gromacs > > Sure, possible. > > But if you want to type the coordinates for FCC lattice using 500 > atoms by hand, that's indeed cool. > > > > On Fri, May 25, 2012 at 11:31 AM, ahmed sta wrote: >> I thought that it is possible to use text editor in order to fix the >> geometry, isn't it? >> >> >> >> De : Dr. Vitaly V. Chaban >> À : ahmed sta >> Cc : gmx-users@gromacs.org >> Envoyé le : Vendredi 25 mai 2012 18h15 >> Objet : Re: Re : Re : Gromacs >> >> Writing your program has nothing to do with gromacs. If you do not >> have experience in programming by far, it may be faster to use the >> second route. But of you still want to generate a program yourself, I >> am delighted to direct your attention to the PYTHON, python.org, >> programming language. >> >> I am aware of some commercial software like MedeA and (perhaps?) >> Materials Studio, capable to generate molecular configurations of >> various symmetries. Maybe, someone in the gromacs mailing list can >> suggest a free alternative as well. >> >> >> >> On Fri, May 25, 2012 at 11:05 AM, ahmed sta wrote: >>> Well i see >>> >>> I think that writing my own program would be better and more accurate >>> How should i proceed ? >>> it is my first use of Gromacs and i do not know how to do >>> >>> Regards >>> >>> >>> De : Dr. Vitaly V. Chaban >>> À : ahmed sta >>> Cc : gmx-users@gromacs.org >>> Envoyé le : Vendredi 25 mai 2012 17h58 >>> Objet : Re: Re : Gromacs >>> >>> If you want a solid system, where atoms are arranged as in FCC, this >>> is another talk. >>> >>> There two way to achieve your goal. Either -- >>> >>> 1) you write a simple program which places argon atoms as in FCC. >>> >>> OR >>> >>> 2) you try to freeze my system into your system using simulated >>> annealing implemented in gromacs. Provided that argon is a pretty >>> simple system, this should not take too much time. At least, I can say >>> that our students get it (216 atoms) freezed during one laboratory >>> work. >>> >>> BTW, there is no guarantee that the freezing point of the classical >>> argon model is perfectly reproduced. My guess is based on the fact >>> that the density of the liquid phase (in the NPT ensemble) is not >>> ideal. >>> >>> >>> Dr. Vitaly V. Chaban, 430 Hutchison Hall >>> Dept. Chemistry, University of Rochester >>> 120 Trustee Road, Rochester, NY 14627-0216 >>> THE UNITED STATES OF AMERICA >>> >>> >>> >>> On Fri, May 25, 2012 at 10:44 AM, ahmed sta >>> wrote: >>>> Sorry. My aim is to model FCC Argon (not liquid state) and i am trying >>>> to >>>> define that geometry >>>> Can you help me please? >>>> >>>> Regards >>>> >>>> >>>> De : Dr. Vitaly V. Chaban >>>> À : ahmed sta >>>> Cc : gmx-users@gromacs.org >>>> Envoyé le : Vendredi 25 mai 2012 17h36 >>>> Objet : Re: Gromacs >>>> >>>> Dear Ahmed - >>>> >>>> I do not understand how you imagine "FCC geometry" in the liquid state >>>> of matter. >>>> >>>> If you want to just resize my system, use the standard "genbox" >>>> utility and then re-equilibrate at the desired temperature and density >>>> (if you want to fix density, of course). >>>> >>>> >>>> Dr. Vitaly V. Chaban, 430 Hutchison Hall >>>> Dept. Chemistry, University of Rochester >>>> 120 Trustee Road, Rochester, NY 14627-0216 >>>> THE UNITED STATES OF AMERICA >>>> >>>> >>>> >>>> On Fri, May 25, 2012 at 10:30 AM, ahmed sta &g
[gmx-users] Re: Re : Re : Gromacs
Writing your program has nothing to do with gromacs. If you do not have experience in programming by far, it may be faster to use the second route. But of you still want to generate a program yourself, I am delighted to direct your attention to the PYTHON, python.org, programming language. I am aware of some commercial software like MedeA and (perhaps?) Materials Studio, capable to generate molecular configurations of various symmetries. Maybe, someone in the gromacs mailing list can suggest a free alternative as well. On Fri, May 25, 2012 at 11:05 AM, ahmed sta wrote: > Well i see > > I think that writing my own program would be better and more accurate > How should i proceed ? > it is my first use of Gromacs and i do not know how to do > > Regards > > ________ > De : Dr. Vitaly V. Chaban > À : ahmed sta > Cc : gmx-users@gromacs.org > Envoyé le : Vendredi 25 mai 2012 17h58 > Objet : Re: Re : Gromacs > > If you want a solid system, where atoms are arranged as in FCC, this > is another talk. > > There two way to achieve your goal. Either -- > > 1) you write a simple program which places argon atoms as in FCC. > > OR > > 2) you try to freeze my system into your system using simulated > annealing implemented in gromacs. Provided that argon is a pretty > simple system, this should not take too much time. At least, I can say > that our students get it (216 atoms) freezed during one laboratory > work. > > BTW, there is no guarantee that the freezing point of the classical > argon model is perfectly reproduced. My guess is based on the fact > that the density of the liquid phase (in the NPT ensemble) is not > ideal. > > > Dr. Vitaly V. Chaban, 430 Hutchison Hall > Dept. Chemistry, University of Rochester > 120 Trustee Road, Rochester, NY 14627-0216 > THE UNITED STATES OF AMERICA > > > > On Fri, May 25, 2012 at 10:44 AM, ahmed sta wrote: >> Sorry. My aim is to model FCC Argon (not liquid state) and i am trying to >> define that geometry >> Can you help me please? >> >> Regards >> >> >> De : Dr. Vitaly V. Chaban >> À : ahmed sta >> Cc : gmx-users@gromacs.org >> Envoyé le : Vendredi 25 mai 2012 17h36 >> Objet : Re: Gromacs >> >> Dear Ahmed - >> >> I do not understand how you imagine "FCC geometry" in the liquid state >> of matter. >> >> If you want to just resize my system, use the standard "genbox" >> utility and then re-equilibrate at the desired temperature and density >> (if you want to fix density, of course). >> >> >> Dr. Vitaly V. Chaban, 430 Hutchison Hall >> Dept. Chemistry, University of Rochester >> 120 Trustee Road, Rochester, NY 14627-0216 >> THE UNITED STATES OF AMERICA >> >> >> >> On Fri, May 25, 2012 at 10:30 AM, ahmed sta wrote: >>> Dear Vitaly >>> >>> >>> I am an engineer student and i am now trying to use Gromacs >>> I found your Argon molecule defined topology created in May 2009 >>> I want to ask you how to define my own geometry on Gromacs >>> In fact i am trying to define liquid Argon system with a density >>> equilibrated at 90K. My system should have a FCC geometry and containing >>> for >>> example 500 atoms >>> >>> >>> I really need your help >>> >>> Best regards >>> >>> >>> >>> >>> Ahmed Sta >>> Ensta Paristech engineering school >>> ahmedsta6...@yahoo.fr >> >> > > -- 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] Re: Re : Gromacs
If you want a solid system, where atoms are arranged as in FCC, this is another talk. There two way to achieve your goal. Either -- 1) you write a simple program which places argon atoms as in FCC. OR 2) you try to freeze my system into your system using simulated annealing implemented in gromacs. Provided that argon is a pretty simple system, this should not take too much time. At least, I can say that our students get it (216 atoms) freezed during one laboratory work. BTW, there is no guarantee that the freezing point of the classical argon model is perfectly reproduced. My guess is based on the fact that the density of the liquid phase (in the NPT ensemble) is not ideal. Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA On Fri, May 25, 2012 at 10:44 AM, ahmed sta wrote: > Sorry. My aim is to model FCC Argon (not liquid state) and i am trying to > define that geometry > Can you help me please? > > Regards > > ________ > De : Dr. Vitaly V. Chaban > À : ahmed sta > Cc : gmx-users@gromacs.org > Envoyé le : Vendredi 25 mai 2012 17h36 > Objet : Re: Gromacs > > Dear Ahmed - > > I do not understand how you imagine "FCC geometry" in the liquid state > of matter. > > If you want to just resize my system, use the standard "genbox" > utility and then re-equilibrate at the desired temperature and density > (if you want to fix density, of course). > > > Dr. Vitaly V. Chaban, 430 Hutchison Hall > Dept. Chemistry, University of Rochester > 120 Trustee Road, Rochester, NY 14627-0216 > THE UNITED STATES OF AMERICA > > > > On Fri, May 25, 2012 at 10:30 AM, ahmed sta wrote: >> Dear Vitaly >> >> >> I am an engineer student and i am now trying to use Gromacs >> I found your Argon molecule defined topology created in May 2009 >> I want to ask you how to define my own geometry on Gromacs >> In fact i am trying to define liquid Argon system with a density >> equilibrated at 90K. My system should have a FCC geometry and containing >> for >> example 500 atoms >> >> >> I really need your help >> >> Best regards >> >> >> >> >> Ahmed Sta >> Ensta Paristech engineering school >> ahmedsta6...@yahoo.fr > > -- 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] Re: Re : Re : Re : Gromacs
Sure, possible. But if you want to type the coordinates for FCC lattice using 500 atoms by hand, that's indeed cool. On Fri, May 25, 2012 at 11:31 AM, ahmed sta wrote: > I thought that it is possible to use text editor in order to fix the > geometry, isn't it? > > > ____________ > De : Dr. Vitaly V. Chaban > À : ahmed sta > Cc : gmx-users@gromacs.org > Envoyé le : Vendredi 25 mai 2012 18h15 > Objet : Re: Re : Re : Gromacs > > Writing your program has nothing to do with gromacs. If you do not > have experience in programming by far, it may be faster to use the > second route. But of you still want to generate a program yourself, I > am delighted to direct your attention to the PYTHON, python.org, > programming language. > > I am aware of some commercial software like MedeA and (perhaps?) > Materials Studio, capable to generate molecular configurations of > various symmetries. Maybe, someone in the gromacs mailing list can > suggest a free alternative as well. > > > > On Fri, May 25, 2012 at 11:05 AM, ahmed sta wrote: >> Well i see >> >> I think that writing my own program would be better and more accurate >> How should i proceed ? >> it is my first use of Gromacs and i do not know how to do >> >> Regards >> >> >> De : Dr. Vitaly V. Chaban >> À : ahmed sta >> Cc : gmx-users@gromacs.org >> Envoyé le : Vendredi 25 mai 2012 17h58 >> Objet : Re: Re : Gromacs >> >> If you want a solid system, where atoms are arranged as in FCC, this >> is another talk. >> >> There two way to achieve your goal. Either -- >> >> 1) you write a simple program which places argon atoms as in FCC. >> >> OR >> >> 2) you try to freeze my system into your system using simulated >> annealing implemented in gromacs. Provided that argon is a pretty >> simple system, this should not take too much time. At least, I can say >> that our students get it (216 atoms) freezed during one laboratory >> work. >> >> BTW, there is no guarantee that the freezing point of the classical >> argon model is perfectly reproduced. My guess is based on the fact >> that the density of the liquid phase (in the NPT ensemble) is not >> ideal. >> >> >> Dr. Vitaly V. Chaban, 430 Hutchison Hall >> Dept. Chemistry, University of Rochester >> 120 Trustee Road, Rochester, NY 14627-0216 >> THE UNITED STATES OF AMERICA >> >> >> >> On Fri, May 25, 2012 at 10:44 AM, ahmed sta wrote: >>> Sorry. My aim is to model FCC Argon (not liquid state) and i am trying to >>> define that geometry >>> Can you help me please? >>> >>> Regards >>> >>> >>> De : Dr. Vitaly V. Chaban >>> À : ahmed sta >>> Cc : gmx-users@gromacs.org >>> Envoyé le : Vendredi 25 mai 2012 17h36 >>> Objet : Re: Gromacs >>> >>> Dear Ahmed - >>> >>> I do not understand how you imagine "FCC geometry" in the liquid state >>> of matter. >>> >>> If you want to just resize my system, use the standard "genbox" >>> utility and then re-equilibrate at the desired temperature and density >>> (if you want to fix density, of course). >>> >>> >>> Dr. Vitaly V. Chaban, 430 Hutchison Hall >>> Dept. Chemistry, University of Rochester >>> 120 Trustee Road, Rochester, NY 14627-0216 >>> THE UNITED STATES OF AMERICA >>> >>> >>> >>> On Fri, May 25, 2012 at 10:30 AM, ahmed sta >>> wrote: >>>> Dear Vitaly >>>> >>>> >>>> I am an engineer student and i am now trying to use Gromacs >>>> I found your Argon molecule defined topology created in May 2009 >>>> I want to ask you how to define my own geometry on Gromacs >>>> In fact i am trying to define liquid Argon system with a density >>>> equilibrated at 90K. My system should have a FCC geometry and containing >>>> for >>>> example 500 atoms >>>> >>>> >>>> I really need your help >>>> >>>> Best regards >>>> >>>> >>>> >>>> >>>> Ahmed Sta >>>> Ensta Paristech engineering school >>>> ahmedsta6...@yahoo.fr >>> >>> >> >> > > -- Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: Gromacs
Dear Ahmed - I do not understand how you imagine "FCC geometry" in the liquid state of matter. If you want to just resize my system, use the standard "genbox" utility and then re-equilibrate at the desired temperature and density (if you want to fix density, of course). Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA On Fri, May 25, 2012 at 10:30 AM, ahmed sta wrote: > Dear Vitaly > > > I am an engineer student and i am now trying to use Gromacs > I found your Argon molecule defined topology created in May 2009 > I want to ask you how to define my own geometry on Gromacs > In fact i am trying to define liquid Argon system with a density > equilibrated at 90K. My system should have a FCC geometry and containing for > example 500 atoms > > > I really need your help > > Best regards > > > > > Ahmed Sta > Ensta Paristech engineering school > ahmedsta6...@yahoo.fr -- 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] Re: Pressure at constant volume
> Hello everyone, > > I am trying to estimate the thermodynamic expression, dP/dw at > constant V and T, for my polymer-solvent system. Where P is the Hello J. - > pressure, w is the mass fraction, V volume and T temperature. I guess > this task can not be done by MD, as for constant Volume, pressure is > meaningless. Since what g_energy reports is not the actual pressure > which corresponds to that fixed Volume. Am I correct? I do not think you are correct here. My belief is that your pressure is just very uncertain for a [relatively] small simulated system. > (I mean building different binary systems with different mass > fractions of w, and measuring average P (dP/dw) while keeping T and V > constant does not produce meaningful results by MD) I think you have just to increase sampling to get trustworthy pressures for a range of your systems. Vitaly Chaban Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: Proper 1-octanol box preparation
Dear Ondrej - I would start with a high pressure simulation (say, P=100 bar) for 200-500 ps. After this run, the system will be compressed to its more realistic liquid density. Then, go back to P=1 bar and re-equilibrate for 100-200 ps. I guess, if the temperature were higher, the density would converge faster. What is the shear viscosity of octanol, something around 5-10 cP? Regards, Vitaly Chaban -- Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA > I prepared a box of 125 1-octanol molecules using genconf -f > octanol_single_molecule.gro -nbox 5 5 5 and I tried to equilibrate > this system in NPT ensemble to get proper density and nice cube box, > similar to octanol configuration that one can download from > http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies. > But I always got something completely different. Some cluster of the > molecules at the bottom of the simulation box, far away from dense > cube configuration. You can see picture here: > https://picasaweb.google.com/okroutil/Science#5738216101659210130. I > tried different thermo- and barostats, different coupling times, > compressibility, first NVT then NPT equil., but with no success. I > also tried more "chaotic" initial configuration generated with genbox > -ci ...gro - nmol 125 -box 5 5 5, no success. > So my question is: is there some simulation protocol or some setting > (higher pressure at the beginning of equilibration?), any trick > suitable for this type of solvent? Till now I worked only with water > and surfaces, so this is new area for me... > > Thank you very much for any answer and have a nice day! > > Ondrej Kroutil (Faculty of Health and Social Studies, South Bohemian > University, Czech Republic) > > P.S.: I used gaff ff and topologies downloaded from > http://virtualchemistry.org/molecules/111-87-5/index.php and this NPT > eq. input: > > integrator = md > dt = 0.002 > nsteps = 50 > comm_mode = linear > nstcomm = 1000 > nstxout = 0 > nstxtcout = 100 > nstvout = 0 > nstfout = 0 > nstlog = 500 > nstlist = 10 > ns_type = grid > rlist = 1.4 > coulombtype = PME > rcoulomb = 1.4 > rvdw = 1.4 > constraints = none > constraint_algorithm = lincs > ;shake_tol = 0.1 > lincs_iter = 1 > fourierspacing = 0.1 > pme_order = 4 > ewald_rtol = 1e-5 > ewald_geometry = 3d > optimize_fft = yes > ; Nose-Hoover temperature coupling > Tcoupl = berendsen > tau_t = 1 > tc_grps = system > ref_t = 298. > ; No Pressure > Pcoupl = berendsen > pcoupltype = isotropic > tau_p = 0.5 > compressibility = 4.6e-5 > ref_p = 1.0 > ; OTHER > periodic_molecules = no > pbc = xyz > gen_vel = yes > gen_temp = 298.15 > gen_seed = -1-- > > > Ondřej Kroutil -- 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] Re: why it is so slow in Blue gene
> hello: > > I am running a 60,000 atom system with 128 core in a blue gene > cluster. and it is only 1ns/day here is the script I used for > submitting jobs: > > # @ job_name = gmx_test > # @ class = kdm-large > # @ error = gmx_test.err > # @ output = gmx_test.out > # @ wall_clock_limit = 00:20:00 > # @ job_type = bluegene > # @ bg_size = 32 > # @ queue > mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum -dlb yes > -v -s npt > _01.tpr -o npt_01.trr -cpo npt_01.cpt -g npt_01.log -launch -nt" -mode > VN -np 128 > > > > here is my npt.mdp > > title = NPT-01 > cpp = /usr/bin/cpp > include = > define = -DPOSRES -DPOSRES_POPE_HEAD > integrator = md > dt = 0.001 > nsteps = 500 > nstxout = 10 > nstvout = 10 > nstlog = 10 > nstenergy = 5 > nstxtcout = 5 > xtc_grps = > energygrps = Protein SOL ION > nstcalcenergy = 10 > nstlist = 10 > nstcomm = 10 > comm_mode = Linear > comm-grps = Protein_POPE Water_and_ions > ns_type = grid > rlist = 1.2 > rlistlong = 1.4 > vdwtype = Switch > rvdw = 1.2 > rvdw_switch = 0.8 > coulombtype = pme > rcoulomb = 1.2 > rcoulomb_switch = 0.0 > fourierspacing = 0.15 > pme_order = 6 > DispCorr = no > tcoupl = V-rescale ;nose-hoover > nhchainlength = 1 > tc-grps = Protein_POPE Water_and_ions > tau_t = 0.1 0.1 > ref_t = 310 310 > Pcoupl = berendsen ;parrinello-rahman > Pcoupltype = semiisotropic > tau_p = 1.0 > compressibility = 4.5e-5 4.5e-5 > ref_p = 1.0 1.0 > pbc = xyz > refcoord_scaling = com > gen_vel = no > optimize_fft = no > constraints = hbonds > constraint_algorithm = Lincs > > Does anybody have any advices? Albert - What is the speed using serial gromacs for the same system? Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: jobs failed
> Hello: > I am using the following script to run Gromacs in cluster, but it failed: > > # @ job_name = bm > # @ class = kdm-large > # @ error = gromacs.info > # @ output = gromacs.out > # @ environment = COPY_ALL > # @ wall_clock_limit = 10:00:00 > # @ notification = error > # @ job_type = bluegene > # @ bg_size = 64 > # @ queue > mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-v -s md.tpr -o > md.trr -cpo md.cpt -c md.gro -g md-out.log -launch" -mode VN -np 256 > > > and here is the log file > > > Back Off! I just backed up md-out.log to ./#md-out.log.1# > Getting Loaded... > Reading file md.tpr, VERSION 4.5.5 (single precision) > Loaded with Money > > > Will use 192 particle-particle and 64 PME only nodes > This is a guess, check the performance at the end of the log file > Making 3D domain decomposition 8 x 4 x 6 > > Back Off! I just backed up md.trr to ./#md.trr.2# > > Back Off! I just backed up traj.xtc to ./#traj.xtc.3# > > Back Off! I just backed up ener.edr to ./#ener.edr.3# > > WARNING: This run will generate roughly 3302 Mb of data > > starting mdrun 'BmEH-complex-POA in water' > 5000 steps, 10.0 ps. > step 0 > > NOTE: Turning on dynamic load balancing > > vol 0.41 imb F 18% pme/F 0.61 step 100, will finish Tue Apr 17 13:49:51 > 2012 > vol 0.42 imb F 12% pme/F 0.60 step 200, will finish Sun Apr 15 23:46:30 > 2012 > vol 0.44 imb F 12% pme/F 0.57 step 300, will finish Sun Apr 15 12:20:49 > 2012 > vol 0.45 imb F 12% pme/F 0.58 step 400, will finish Sun Apr 15 07:01:25 > 2012 > vol 0.48 imb F 12% pme/F 0.57 step 500, will finish Sun Apr 15 03:46:13 > 2012 > vol 0.49! imb F 11% pme/F 0.57 step 600, will finish Sun Apr 15 01:43:05 > 2012 > vol 0.46! imb F 10% pme/F 0.59 step 700, will finish Sun Apr 15 00:01:14 > 2012 > vol 0.42! imb F 10% pme/F 0.58 step 800, will finish Sat Apr 14 22:56:06 > 2012 > vol 0.45! imb F 12% pme/F 0.56 step 900, will finish Sat Apr 14 22:16:49 > 2012 > vol 0.46! imb F 10% pme/F 0.57 step 1000, will finish Sat Apr 14 > 21:49:10 2012 > vol 0.46! imb F 9% pme/F 0.58 step 1100, will finish Sat Apr 14 > 21:26:04 2012 > vol 0.47! imb F 10% pme/F 0.57 step 1200, will finish Sat Apr 14 > 21:02:35 2012 > vol 0.45 imb F 9% pme/F 0.58 step 1300, will finish Sat Apr 14 > 20:34:22 2012 > vol 0.45! imb F 9% pme/F 0.58 step 1400, will finish Sat Apr 14 > 20:15:54 2012 > vol 0.48! imb F 11% pme/F 0.57 step 1500, will finish Sat Apr 14 > 20:07:48 2012 > vol 0.47! imb F 10% pme/F 0.58 step 1600, will finish Sat Apr 14 > 19:57:46 2012 > vol 0.47! imb F 13% pme/F 0.58 step 1700, will finish Sat Apr 14 > 19:51:47 2012 > vol 0.45! imb F 11% pme/F 0.58 step 1800, will finish Sat Apr 14 > 19:44:37 2012 > vol 0.46! imb F 13% pme/F 0.57 step 1900, will finish Sat Apr 14 > 19:37:10 2012 > vol 0.50! imb F 12% pme/F 0.58 step 2000, will finish Sat Apr 14 > 19:29:20 2012 > vol 0.50! imb F 12% pme/F 0.58 step 2100, will finish Sat Apr 14 > 19:23:00 2012 > vol 0.48 imb F 10% pme/F 0.57 step 2200, will finish Sat Apr 14 > 19:15:43 2012 > vol 0.50! imb F 11% pme/F 0.57 step 2300, will finish Sat Apr 14 > 19:13:30 2012 > vol 0.49! imb F 11% pme/F 0.57 step 2400, will finish Sat Apr 14 > 19:10:14 2012 > vol 0.48 imb F 10% pme/F 0.58 step 2500, will finish Sat Apr 14 > 19:01:51 2012 > vol 0.47! imb F 12% pme/F 0.58 step 2600, will finish Sat Apr 14 > 18:55:11 2012 > vol 0.48! imb F 11% pme/F 0.58 step 2700, will finish Sat Apr 14 > 18:49:47 2012 > vol 0.46! imb F 12% pme/F 0.58 step 2800, will finish Sat Apr 14 > 18:45:32 2012 Check what happens to your volume. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: hkl harker sections
> Hello all, > > Does anyone know where to look to do a slice of my unit cell along sections > (energies, forces etc...) or to just give a list of all atoms in the slice. > Something like an h,k,l or x,y,z slice through a section. > > Stephan Watkins > -- I believe the only way is to construct the index file by hand. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: large scale simulations
> thank you very much for your kind comments. Probably the most > effective way is to optimize PME balance as Mark mentioned. It seems The "most effective way" to get very quick simulations of the large systems is to avoid PME It is up to the researcher to ensure good accuracy anyway. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: how to optimize hydrogen bonds before simulation?
> > Hello: > > I am wondering is it possible to optimize hydrogen bonds network > before simulation? I've got some crystal solvent in the system and I > would like to optimize the hbond network even before building a solvent > system. If you freeze all atoms which are not involved in H-bonds, the coordinates of the remaining atoms will be optimized. Another question is why you need that "before building a solvent". Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: crazy temperatures
> Dear GMCS users > > Hi. Does anyone know if MD at 2K is feasible? Aggregate state, not temperature, matters if you want to discuss potential models applicability. I believe at ~10,000K one can get quite realistic results for the gaseous phase of certain high-melting substances like CaO or MgS. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re:200 CPU, 3ns/day for 80,000 atoms
> I am using gromacs for membrane simulation (under CHARMM36 FF) which > contains around 80,000 atoms. I've submitted over 200 CPU in the cluster > for such system with 2 fs time step. And what really astonished is that the > efficiency for such simulation is only 3ns/day. I am wondering what > happen to my system or gromacs? What can I do to fasten the simulation? > > here is my md.mdp: > * > title = god! > cpp = /usr/bin/cpp > include = > define = > integrator = md > dt = 0.001 > nsteps = 1 > nstxout = 100 > nstvout = 100 > nstlog = 100 > nstenergy = 1 > nstxtcout = 10 > xtc_grps = > energygrps = Protein POPC SOL ION > nstcalcenergy = 1 > nstlist = 1 > nstcomm = 1 > comm_mode = Linear > comm-grps = Protein_POPC Water_and_ions > ns_type = grid > rlist = 1.2 > rlistlong = 1.4 > vdwtype = Switch > rvdw = 1.2 > rvdw_switch = 0.8 > coulombtype = pme > rcoulomb = 1.2 > rcoulomb_switch = 0.0 > fourierspacing = 0.15 > pme_order = 4 > DispCorr = no > tcoupl = nose-hoover > nhchainlength = 1 > tc-grps = Protein_POPC Water_and_ions > tau_t = 0.5 0.5 > ref_t = 310 310 > Pcoupl = parrinello-rahman > Pcoupltype = semiisotropic > tau_p = 5.0 > compressibility = 4.5e-5 4.5e-5 > ref_p = 1.0 1.0 > pbc = xyz > gen_vel = no > optimize_fft = no > constraints = hbonds > constraint_algorithm = Lincs > * This discussion should be started with you reporting the speedup for your system with 200cpu's. Rather than appealing just to some velocity per nanosecond. Neighborsearching is inefficient. Outputting immediate velocities every 100 steps is senseless. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] electrostatics in liquid/vapor interface
Dear All -- I have a system of the liquid/vapor interface kind. The droplet of liquid with a radius of about 10nm is surrounded by a volume of vacuum of ~1000nm^3. What is the best method among those currently in GROMACS4 to treat electrostatics in this case? Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: Simulated Annealing Protocol
x > lincs_iter = 1 ; number of iterations > to correct for rotational lengthening > lincs_warnangle = 30 ; [degrees] maximum angle that > a bond can rotate before LINCS will complain > > My Queries > > 1. Is My mdp file ok ???..please give me a nice protocol.. > 2.. Should I have to do position restrained MD before SA(simulated annealing) > (If yes then what the temp. should I have to used for NVT and NPT > (as in mdp file has lower 5 K and high 300 k ) ) > Your system will be heated from 5 to 330K during 20ps. If this is what you want, than it is correct. I would, however, prefer slower heating in order to make it more realistic. I see no obvious necessity to start from restrained positions, unless you are going to performs something specific that you did not describe above. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: on the RAM capacity needed for GROMACS
> Dear All, > > Suppose I need to install the GROMACS in my laptop. Will you please tell me > the requirement on the capacity of RAM? > I still did not invent a system that would not run on my 8GB RAM laptop. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: Resources on simulation walls
> Hi, > > Only if you have time, do you know of any resources that explain the concept > of a Gromacs wall, which seems related to 2-D Ewald summation? In the > Gromacs 4.5.4 manual, the parameters related to walls are described on page > 182, and also on http://manual.gromacs.org/current/online/mdp_opt.html#walls > . But do you know of any general explanations, books, or literature papers > that would help me to understand what a wall does and why and when I need to > use them? I cannot seem to find them discussed in the main Gromacs papers ( > http://www.gromacs.org/Documentation/Gromacs_papers ). > > Also, is there another name for a simulation wall? When I use Google to > search for "MD simulation wall", it is not clear that I am looking for the > correct thing. > If I recollect correctly, the gromacs wall provides elastic collision for the particles approaching it. There was some discussion of this matter in this list around February-March, 2009, browse archives... -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] writing checkpoints
We are running quite a large system with a default checkpoint intervals (15 minutes). However, in the md.log file, it is written like below Writing checkpoint, step 138 at Thu Jan 19 11:00:36 2012 Writing checkpoint, step 1380010 at Thu Jan 19 11:00:41 2012 Writing checkpoint, step 1380020 at Thu Jan 19 11:00:46 2012 Writing checkpoint, step 1380030 at Thu Jan 19 11:00:51 2012 Writing checkpoint, step 1380040 at Thu Jan 19 11:00:55 2012 Writing checkpoint, step 1380050 at Thu Jan 19 11:01:00 2012 Then after an hour - Writing checkpoint, step 139 at Thu Jan 19 12:21:18 2012 Writing checkpoint, step 1390010 at Thu Jan 19 12:21:23 2012 Writing checkpoint, step 1390020 at Thu Jan 19 12:21:28 2012 Writing checkpoint, step 1390030 at Thu Jan 19 12:21:32 2012 The job is executed using 4 cores. The version is 4-0-7. Is this a bug? Just curious. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: LINCS warnings and number of cpus
> > Dear users, > I would like to ask your help about understanding a problem i'm not able > to recognize by myself. > Basically, a user of our sistem (IBM SP6, power6 architecture) is trying > to run a simulation of a very simple sistem, a polymer chain in a lot of > water molecules. While the simulation works perfectly in serial on her > local pc, when she tries to run it in SP6 using 2 cpus in parallel, the > simulation doesn't even start due of these errors: > > /starting mdrun 'PVA head29tail in water' > 250 steps, 5000.0 ps. > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 83427404711319.468750, max 431899260485632.00 (between atoms 59 > and 60) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 37 38 89.6 0.1530 124222742528. 0.1530 > 38 41 89.1 0.1530 104382357504. 0.1530 > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 56829711484907.867188, max 212898492186624.00 (between atoms 3 > and 4) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 61 62 89.0 0.1530 1380386603008. 0.1530 > 58 61 87.6 0.1530 669758914560. 0.1530 > 58 59 89.2 0.1430 1994809540608. 0.1430 > 59 60 90.0 0.1000 43189926887424. 0.1000 > 57 58 88.3 0.1530 1126801342464. 0.1530 > 54 57 85.9 0.1530 198269452288. 0.1530 > 54 55 89.6 0.1430 1261346488320. 0.1430 > 38 39 89.6 0.1430 156364750848. 0.1430 > 39 40 90.0 0.1000 3183089549312. 0.1000 > // [...] > 18 21 89.9 0.1530 215265542144. 0.1530 > 18 19 90.0 0.1430 872386920448. 0.1430 > 19 20 90.0 0.1000 6085561286656. 0.1000 > 95 96 90.0 0.1000 5006930477056. 0.1000 > 97 98 89.7 0.1530 215830478848. 0.1530 > 98 101 90.5 0.1530 232671739904. 0.1530 > 98 99 90.0 0.1430 746076962816. 0.1430 > 99 100 90.0 0.1000 6068662435840. 0.1000 > step 0: Water molecule starting at atom 6014 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > step 0: Water molecule starting at atom 7355 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > Wrote pdb files with previous and current coordinates > Wrote pdb files with previous and current coordinates > step 0 > Warning: 1-4 interaction between 37 and 40 at distance 3039839053625.364 > which is larger than the 1-4 table size 2.200 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > Warning: 1-4 interaction between 61 and 64 at distance > 15924520737123.646 which is larger than the 1-4 table size 2.200 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > ERROR: 0031-250 task 0: Segmentation fault > ERROR: 0031-250 task 1: Segmentation fault > > /The same errors occur when trying the simulation up to 4 cpus, but (and > that's the strange thing), everything works fine with 6+ cpus (actually, > there are some numbers giving an incompatibility error, like /"There is > no domain decomposition for 7 nodes that is compatible with the given > box and a minimum cell size of 0.95625 nm"/, but for example 6 or 8 cpus > give a successful run). > > Can anyone understand what is the reason of this strange behaviour? > Thanks, > Marani Alessandro (HPC User support, CINECA - Italy) Hmm... Try "mdrun -pd %NUMPROC" -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: cnt topology
I hope you understand that I canNOT fix the problem by just looking at several thousands on numbers in your topology... My preliminary guess would be that the problem is localized in the dihedral section, i.e. you don't define all the necessary dihedrals or define some of them inconsistently with your GRO file. I would start with visualizing you GRO including atom numbers and checking manually if all the dihedrals you actually see are present in the topology file. Usually, considering the very first circle of the carbon atoms will give your an answer. There is also a lazy solution. If you don't need a flexible tube, you can just freeze its carbon atoms (in the MDP file), so that the geomerty will be stable at all times -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA On Sat, Dec 31, 2011 at 1:42 PM, Zahra M wrote: > sorry I forget to attach my cnt topology file > > ____ > From: Dr. Vitaly V. Chaban > To: Zahra M > Cc: gmx-users@gromacs.org > Sent: Saturday, December 31, 2011 8:51 PM > Subject: Re: > > Zahra: > > I believe the problem is in your topology (*.TOP) file which you don't > attach. From your pictures, we see that the system does not survive > energy minimization, so the intramolecular interactions are not > simulated wisely. > > Happy New Year, > > Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. > Univ. Rochester, Rochester, New York 14627-0216 > THE UNITED STATES OF AMERICA > > > > On Sat, Dec 31, 2011 at 11:58 AM, Zahra M wrote: >> Hi dear Dr. Vitaly >> I'm simulating a system containing CNT and a protein with GROMACS, and I >> encounter with some problems, as I understood (by reading articles) you've >> worked on CNT simulation alot, so I decided to ask you for help. I wish >> you >> help me to solve my problem. >> As I mentioned my system contains CNT and protein, in a dodecahedron unit >> cell. when I run EM (although in vacuum) the shape of CNT changes, and its >> bonds crash. >> here are my MD parameters for EM: >> >> " >> integrator = steep ; Algorithm (steep = steepest descent >> minimization) >> emtol = 1000.0 ; Stop minimization when the maximum force < >> 1000.0 kJ/mol/nm >> emstep = 0.01 ; Energy step size >> nsteps = 5 ; Maximum number of (minimization) steps to >> perform >> nstlist = 1 ; Frequency to update the neighbor list and long >> range forces >> ns_type = grid ; Method to determine neighbor list (simple, >> grid) >> rlist = 1.0 ; Cut-off for making neighbor list (short range >> forces) >> domain-decomposition = no >> coulombtype = PME ; Treatment of long range electrostatic >> interactions >> rcoulomb = 1.0 ; Short-range electrostatic cut-off >> rvdw = 1.0 ; Short-range Van der Waals cut-off >> pbc = xyz ; Periodic Boundary Conditions (yes/no) >> fourierspacing = 0.20 >> " >> >> but when I run mdrun command these lines appear in terminal: >> >> " >> There were 16 inconsistent shifts. Check your topology >> >> ... >> There were 16 inconsistent shifts. Check your topology >> Warning: 1-4 interaction between 418 and 533 at distance 2.620 which is >> larger than the 1-4 table size 2.400 nm >> These are ignored for the rest of the simulation >> This usually means your system is exploding, >> if not, you should increase table-extension in your mdp file >> or with user tables increase the table size >> There were 16 inconsistent shifts. Check your topology 2.27716e+06, atom= >> 536 >> Step= 1, Dmax= 1.0e-02 nm, Epot= 2.74550e+07 Fmax= 2.26527e+06, atom= >> 536 >> There were 16 inconsistent shifts. Check your topology >> Step= 2, Dmax= 1.2e-02 nm, Epot= 2.71314e+07 Fmax= 2.25101e+06, atom= >> 536 >> There were 16 inconsistent shifts. Check your topology >> Step= 3, Dmax= 1.4e-02 nm, Epot= 2.67459e+07 Fmax= 2.23390e+06, atom= >> 536 >> There were 16 inconsistent shifts. Check your topology >> Step= 4, Dmax= 1.7e-02 nm, Epot= 2.62873e+07 Fmax= 2.21339e+06, atom= >> 536 >> There were 16 inconsistent shifts. Check your topology >> Step= 5, Dmax= 2.1e-02 nm, Epot= 2.57427e+07 Fmax= 2.18879e+06, atom= >> 536 >> There were 16 inconsistent shifts. Check your topology >> Step= 6, Dmax= 2.5e-02 nm, Epot= 2.50973e+07 Fmax= 2.15928e+06, atom= >> 536 >> There were 1
[gmx-users] Re:
Zahra: I believe the problem is in your topology (*.TOP) file which you don't attach. From your pictures, we see that the system does not survive energy minimization, so the intramolecular interactions are not simulated wisely. Happy New Year, Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA On Sat, Dec 31, 2011 at 11:58 AM, Zahra M wrote: > Hi dear Dr. Vitaly > I'm simulating a system containing CNT and a protein with GROMACS, and I > encounter with some problems, as I understood (by reading articles) you've > worked on CNT simulation alot, so I decided to ask you for help. I wish you > help me to solve my problem. > As I mentioned my system contains CNT and protein, in a dodecahedron unit > cell. when I run EM (although in vacuum) the shape of CNT changes, and its > bonds crash. > here are my MD parameters for EM: > > " > integrator = steep ; Algorithm (steep = steepest descent > minimization) > emtol = 1000.0 ; Stop minimization when the maximum force < > 1000.0 kJ/mol/nm > emstep = 0.01 ; Energy step size > nsteps = 5 ; Maximum number of (minimization) steps to > perform > nstlist = 1 ; Frequency to update the neighbor list and long > range forces > ns_type = grid ; Method to determine neighbor list (simple, > grid) > rlist = 1.0 ; Cut-off for making neighbor list (short range > forces) > domain-decomposition = no > coulombtype = PME ; Treatment of long range electrostatic > interactions > rcoulomb = 1.0 ; Short-range electrostatic cut-off > rvdw = 1.0 ; Short-range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions (yes/no) > fourierspacing = 0.20 > " > > but when I run mdrun command these lines appear in terminal: > > " > There were 16 inconsistent shifts. Check your topology > > ... > There were 16 inconsistent shifts. Check your topology > Warning: 1-4 interaction between 418 and 533 at distance 2.620 which is > larger than the 1-4 table size 2.400 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > There were 16 inconsistent shifts. Check your topology 2.27716e+06, atom= > 536 > Step= 1, Dmax= 1.0e-02 nm, Epot= 2.74550e+07 Fmax= 2.26527e+06, atom= > 536 > There were 16 inconsistent shifts. Check your topology > Step= 2, Dmax= 1.2e-02 nm, Epot= 2.71314e+07 Fmax= 2.25101e+06, atom= > 536 > There were 16 inconsistent shifts. Check your topology > Step= 3, Dmax= 1.4e-02 nm, Epot= 2.67459e+07 Fmax= 2.23390e+06, atom= > 536 > There were 16 inconsistent shifts. Check your topology > Step= 4, Dmax= 1.7e-02 nm, Epot= 2.62873e+07 Fmax= 2.21339e+06, atom= > 536 > There were 16 inconsistent shifts. Check your topology > Step= 5, Dmax= 2.1e-02 nm, Epot= 2.57427e+07 Fmax= 2.18879e+06, atom= > 536 > There were 16 inconsistent shifts. Check your topology > Step= 6, Dmax= 2.5e-02 nm, Epot= 2.50973e+07 Fmax= 2.15928e+06, atom= > 536 > There were 16 inconsistent shifts. Check your topology > Step= 7, Dmax= 3.0e-02 nm, Epot= 2.43348e+07 Fmax= 2.12391e+06, atom= > 536 > There were 16 inconsistent shifts. Check your topology > Step= 8, Dmax= 3.6e-02 nm, Epot= 2.34369e+07 Fmax= 2.08150e+06, atom= > 536 > There were 16 inconsistent shifts. Check your topology > Step= 9, Dmax= 4.3e-02 nm, Epot= 2.23854e+07 Fmax= 2.03066e+06, atom= > 536 > There were 16 inconsistent shifts. Check your topology > Step= 10, Dmax= 5.2e-02 nm, Epot= 2.11653e+07 Fmax= 1.96974e+06, atom= > 536 > There were 16 inconsistent shifts. Check your topology > Step= 11, Dmax= 6.2e-02 nm, Epot= 1.97571e+07 Fmax= 1.89657e+06, atom= > 536 > There were 16 inconsistent shifts. Check your topology > Step= 12, Dmax= 7.4e-02 nm, Epot= 1.81605e+07 Fmax= 1.80954e+06, atom= > 536 > There were 16 inconsistent shifts. Check your topology > Step= 13, Dmax= 8.9e-02 nm, Epot= 1.63847e+07 Fmax= 1.72347e+06, atom= > 536 > There were 16 inconsistent shifts. Check your topology > Step= 14, Dmax= 1.1e-01 nm, Epot= 1.43324e+07 Fmax= 1.59766e+06, atom= > 536 > There were 16 inconsistent shifts. Check your topology > Step= 15, Dmax= 1.3e-01 nm, Epot= 1.21562e+07 Fmax= 1.45696e+06, atom= > 536 > There were 16 inconsistent shifts. Check your topology > Step= 16, Dmax= 1.5e-01 nm, Epot= 9.93679e+06 Fmax= 1.32228e+06, atom= > 545 > There were 16 inconsistent shifts. Check your topology >
[gmx-users] Re: g_msd and pbc
> > Thanks Tsjerk for the information. It would be very nice if you can > elaborate it. I am unable to understand. > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > > On Thu, Dec 8, 2011 at 12:10 AM, Tsjerk Wassenaar wrote: > >> Hi Chandan, >> >> Pretty simple; you just take the smallest distance between the time >> points in the periodic system. >> >> Cheers, >> >> Tsjerk >> >> On Wed, Dec 7, 2011 at 6:44 PM, Chandan Choudhury >> wrote: >> > >> > Dear gmx_users, >> > >> > I was just wondering how the g_msd (of gmx 4.0.7) code, takes care of the >> > PBC. e.g. If I want to calculate the lateral diffusion of a lipid bilayer >> > and at some point of the trajectory, some lipid molecules, due to PBC in >> the >> > lateral direction, might pop out from one side of the box and re-ener >> from >> > the other side. I such a situation it should show a very lage msd, but >> > actually in the g_msd code, this fact is taken care of. Can some one >> > explain, how is this effect taken care of. >> > In periodic system, there is infinite number of images of each particle. You should always consider the smallest possible distance [between the image of the two particles]. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: grompp error for CNT simulation
> Dear gmx users, > I am using gromacs 4.5.3 to simulate CNT in water. up to now I have done > these things: > 1. I used packmol to create my PDB file and the used editconf to change PDB > to gro file. > 2. I copied oplsaa.ff folder in my working directory > 3. I added following lines to atomname2type.n2t > C opls_995 0 12.011 2 C 0.142 C 0.142 > C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142 > C opls_997 0 12.011 4 C 0.142 C 0.142 C 0.142 C 0.142 > C opls_998 0 12.011 5 C 0.142 C 0.142 C 0.142 C 0.142 C > 0.142 > 4. I added these to atomtypes.atp > opls_995 12.01100 > opls_996 12.01100 > opls_997 12.01100 > opls_998 12.01100 > > 5. I added these to ffbonded.itp > [ bondtypes ] > C C 1 0.14210 478900 > > [ angletypes ] > C C C 1 120.000 397.480 > > [ dihedraltypes ] > C C 1 0.000 167.360 1 > 6. I used g_x2top to create topology for CNT. > Command line was: > > g_x2top -f CNT.gro -o CNT.top -pbc -nopairs -name CNT -nexcl 5 > > 7. I wrote a .top file given below, > ; Include forcefield parameters > #include "./oplsaa.ff/forcefield.itp" > ; Include topology for water > #include "oplsaa.ff/spc.itp" > ; Include topology for CNT > #include "oplsaa.ff/CNT.itp" > > [ system ] > ; Name > SDS and CNT in water > [ molecules ] > ; Compound #mols > water 9000 > CNT 1 > 8. when I run grompp for EM with this command line :grompp -f md.mdp -c > cnt_alone.gro -p topol.top -o em.tpr > it gave me the following error:Atomtype opls_995 not found. > I would be pleased if anyone could help me how to fix this. Maybe the non-found atomtype is really absent? On the gromacs website, there should be some examples for the CNT topologies based on the GROMOS FF. Independently, check your angles once again. It seems, there should be more angles which are to be defined for a tube. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: gmx-users Digest, Vol 91, Issue 191
> > Dear All, > > Is there a way to let GROMACS to calculate and write the total dipole moment > on-the-fly? > > I realize that g_dipoles can be used to calculate the total dipole moment > using a stored trajectory. However, for a large system it is not very > feasible to write the trajectory at a frequency good enough for spectra > analysis. > > Thanks. I don't think such way exists, unless you insert the dipole calculation subroutine into the main code. All gromacs analysis tools imply postprocessing of the generated trajectories. In certain cases (e.g. when velocities or forces should be analyzed), this is not perfect, of course. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: NPT or NVT for calculating averaged experimental parameters
> Hi there, > > Is there any consensus on whether to use NVT or NPT runs for calculating > averaged NMR parameters in water at room temperature? I have seen some > papers which use NPT, others use NVT. > > Thanks you, > Igor There should be no difference as far as the density is reproduced adequately in both ensembles. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] How DispCorr influsnces pressure
Dear all: Could anybody comment about why "DispCorr=EnerPres" influences pressure so drastically? For certain system of liquid/vapor interface, we get P_zz (perpendicular to the interface) = -7 (with correction) and +4 without correction. The statistics is a few nanoseconds, so this cannot be just a result of large fluctuations. Thanks in advance. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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
Re: [gmx-users] barostat for gases
Looks generally reasonable. Thanks! - Vitaly On Tue, Nov 8, 2011 at 12:20 PM, Krzysztof Kuczera wrote: > The ideal gas result is -(1/V)(dV/dp)_T = 1/p , so I suppose the value > should be = 1.0 bar-1 > under standard conditions > Krzysztof > > On 11/8/11 10:51 AM, Dr. Vitaly V. Chaban wrote: >> >> Could anybody please suggest a convenient compressibility value for MD >> boxes of gases (at normal conditions)? >> >> Thanks. >> > > > -- > Krzysztof Kuczera > Departments of Chemistry and Molecular Biosciences > The University of Kansas > 2010 Malott Hall > Lawrence, KS 66045 > Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu > http://oolung.chem.ku.edu/~kuczera/home.html -- 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] barostat for gases
Could anybody please suggest a convenient compressibility value for MD boxes of gases (at normal conditions)? Thanks. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: problem while running production md
> dear gmx-users, > > i am getting the following error message while running production md > (mpirun).. > > > Step 102, time 0.204 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 122.760095, max 2890.435059 (between atoms 5092 and 5090) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 5079 5069 30.7 0.1532 0.1888 0.1522 > 5081 5079 79.8 0.1056 0.2608 0.1335 > 5080 5079 39.1 0.1237 0.1673 0.1229 > 5083 5081 79.7 0.1459 0.8597 0.1449 > 5082 5081 78.7 0.1016 0.1856 0.1010 > 5098 5083 78.5 0.1532 0.7685 0.1522 > 5085 5083 85.9 0.1537 1.9840 0.1526 > 5084 5083 70.4 0.1097 0.4235 0.1090 > 5088 5085 83.6 0.1536 2.4114 0.1526 > 5087 5085 85.9 0.1098 1.5565 0.1090 > 5086 5085 87.3 0.1099 1.2617 0.1090 > 5088 5094 88.6 0.1535 3.0328 0.1526 > Wrote pdb files with previous and current coordinates > Wrote pdb files with previous and current coordinates > Warning: 1-4 interaction between 5093 and 5094 at distance 6.570 which is > larger than the 1-4 table size 2.200 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > > Warning: 1-4 interaction between 5091 and 5094 at distance 2.444 which is > larger than the 1-4 table size 2.200 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size I think your system is not relaxed, so you are NOT actually running "production md". -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: Structure preparation for the simulation
> Dear Gromacs Users! > > > I'd like to know about external software wich could be used for structure > processing for the futher simulation in Gromacs. Today I've tried one of the > most popular such software Amber tools but I've forced with problems during > compilation of it ") So I'm looking for possible analogues ) > > First of all I'm intresting in software for the addition different CAPing > groups to N and C termi of my protein. > > Is there any plugins for Pymol or VMD for such purposes? I've loked for this > option in both of that software but couldnot find > > > Thank you for your help, > > James Among free solutions... maybe this would help: http://www.chemaxon.com/marvin/sketch/index.php I don't know molecular editor plugins for VMD, but it would be cool, if one is accessible. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: Dear Chaban lincs warning
You should provide topology file, I do NOT need your MDP files. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA 2011/10/31 ahmet yıldırım : > Dear Dr. Chaban, > > Firstly, thanks for your reply. I send you the input files that I used. > Please look at attached files. By the way, I am using Gromacs 4.5.3 > > Regards > > > > 30 Ekim 2011 02:53 tarihinde Dr. Vitaly V. Chaban > yazdı: >> >> Hello Ahmet: >> >> The warnings originating from the LINCS algorithm are dee to either >> incorrect topology (TOP file) of certain particle or bad initial >> configuration (GRO file). >> >> If you don't provide this information about your problematic system, >> there is no chance to help you. >> >> -- >> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. >> Univ. Rochester, Rochester, New York 14627-0216 >> THE UNITED STATES OF AMERICA >> >> >> >> 2011/10/29 ahmet yıldırım : >> > Dear Dr. Chaban, >> > >> > I am studying on protein modelling using Gromacs software for 1-2 years. >> > I >> > have lincs warning error. I obtained the error "lincs warning" after >> > "mdrun >> > -deffnm protein-RUN" (finally step). I could not figure out this problem >> > for >> > weeks :-((( >> > >> > If can you help me I will be very very happy? :-( >> > >> > Sincerely yours >> > >> > Department of Physics, Siirt University, Siirt, Turkey >> > >> > -- >> > Dr.Ahmet YILDIRIM >> > > > > > -- > Ahmet YILDIRIM > -- 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] Re: Dear Chaban lincs warning
ahmet yıldırım: If you want a personal mentoria, you will need to pay for it first. If you strive to get a FREE help, all correspondence should be kept in the mailing list to save up an archive for other gromacs users. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA 2011/10/31 ahmet yıldırım : > Please, dont send any reply. I dont want your helps. You send to gmx user > list my mail without permission from me :(:(:(. Please dont send me any > mail/reply > > > > 31 Ekim 2011 09:27 tarihinde ahmet yıldırım yazdı: >> >> Dear Dr. Chaban, >> >> Firstly, thanks for your reply. I send you the input files that I used. >> Please look at attached files. By the way, I am using Gromacs 4.5.3 >> >> Regards >> >> >> >> 30 Ekim 2011 02:53 tarihinde Dr. Vitaly V. Chaban >> yazdı: >>> >>> Hello Ahmet: >>> >>> The warnings originating from the LINCS algorithm are dee to either >>> incorrect topology (TOP file) of certain particle or bad initial >>> configuration (GRO file). >>> >>> If you don't provide this information about your problematic system, >>> there is no chance to help you. >>> >>> -- >>> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. >>> Univ. Rochester, Rochester, New York 14627-0216 >>> THE UNITED STATES OF AMERICA >>> >>> >>> >>> 2011/10/29 ahmet yıldırım : >>> > Dear Dr. Chaban, >>> > >>> > I am studying on protein modelling using Gromacs software for 1-2 >>> > years. I >>> > have lincs warning error. I obtained the error "lincs warning" after >>> > "mdrun >>> > -deffnm protein-RUN" (finally step). I could not figure out this >>> > problem for >>> > weeks :-((( >>> > >>> > If can you help me I will be very very happy? :-( >>> > >>> > Sincerely yours >>> > >>> > Department of Physics, Siirt University, Siirt, Turkey >>> > >>> > -- >>> > Dr.Ahmet YILDIRIM >>> > >> >> >> >> -- >> Ahmet YILDIRIM > > > > -- > Ahmet YILDIRIM > -- 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] Re: Dear Chaban lincs warning
Hello Ahmet: The warnings originating from the LINCS algorithm are dee to either incorrect topology (TOP file) of certain particle or bad initial configuration (GRO file). If you don't provide this information about your problematic system, there is no chance to help you. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA 2011/10/29 ahmet yıldırım : > Dear Dr. Chaban, > > I am studying on protein modelling using Gromacs software for 1-2 years. I > have lincs warning error. I obtained the error "lincs warning" after "mdrun > -deffnm protein-RUN" (finally step). I could not figure out this problem for > weeks :-((( > > If can you help me I will be very very happy? :-( > > Sincerely yours > > Department of Physics, Siirt University, Siirt, Turkey > > -- > Dr.Ahmet YILDIRIM > -- 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] Re:polymer chain length and density
> Dear experts, > > I have a quick and naive inquiry. I see in the molecular dynamics > simulations that density of the polymers increase slightly with increasing > degree of polymerization ( or Mw). Even for the systems having the same > total atom numbers but one with less number of chains of higher Mw. My guess > its because of the less void space in case of higher Mw chains..?! It is because the interatomic distances between chemically bonded atoms are noticeably smaller than between the atoms of just neighboring molecules. I think when you come to publishing your results, you will need to exactly specify the number of monomers in your chain. It may also be interesting to discuss how much your properties are affected by this length. > And usually properties depending on Mw level off with no significant change > in the property of interest vs chain length. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re:Mixing Force Fields
If the [ defaults ] sections are identical, you have just to add the items from [atoms], [bonds], etc sections of the new force field to the appropriate sections of the old force field. The compatibility of these force fields is a sort of magic that is up to you. - Vitaly > I have a general question about mixing force fields. I want to try to > use CGenFF to model the drug and I wanted to use CHARMM for the > solvent. I see the general advice given online is to always use only > one forcefield but I know CGenFF was developed off CHARMM but > specifically for drugs. If anything, I would like to try it to see > how different results are from just using CGenFF. How would one go > about using two forcefields on your topology? For example below, would > one simply add the non-default FF to the default FF? > > ; File 'topol.top' was generated > ; By user: Administrator (500) > ; On host: fabian-3bef2d6a > ; At date: Fri April 1st 02:59 PM 2011 > ; > ; This is your topology file > ; DRUG SOLUTION w/ Ethanol > > ; Include forcefield parameters > #include "Charmm.ff" > #include "Cgenff.ff" > > > **Thanks for everyones help. > > -- > Best regards, > > Fabian F. Casteblanco > Rutgers University -- > Chemical Engineering PhD Student > C: +908 917 0723 > E: fabian.castebla...@gmail.com -- 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] Re: A quick Q: How to get the history in make_ndx
> > How do I use the history input in the make_ndx prompt, > > such as before I input > > name 32 A2 > name 33 A3 > > up arrow showed me: > ^[[A > Alt+up arrow showed me: > ^[[1;3A Such behavior is not programmed. You are welcome to add the necessary part of the code. CTRL+C/V solves the problem. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] g_clustsize and temp.xvg
According to the description of the g_clustsize utility, it should create the file "temp.xvg" containing the temperature of the largest cluster versus time. While other files from g_clustsize are created correctly, the "temp.xvg" is always empty. What is printed follows: --- # This file was created Sun Oct 2 21:08:45 2011 # by the following command: # g_clustsize -n index.ndx # # g_clustsize is part of G R O M A C S: # # Good ROcking Metal Altar for Chronical Sinners # @title "Temperature of largest cluster" @xaxis label "Time (ps)" @yaxis label "T (K)" @TYPE xy --- The invocation line is: g_clustsize -n index.ndx Did anybody see this function working? I am using 4.0.7 version. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: GROMACS @ Facebook
Cool... :-) > Hi, > > for your entertainment and as a reach-out to younger scientists GROMACS > is now on Facebook. Please look us up at: > > http://www.facebook.com/pages/GROMACS/257453660934850 > > We're looking forward to your comments. > > Cheers, > -- > 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.se http://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/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
Re: [gmx-users] Re: energy terms vs. temperature
Justin, I was speaking only about the bonded (and presumably, harmonic) potentials. Decreasing the time-step, as I mentioned, never made the things worse. Vitaly On Tue, Sep 6, 2011 at 7:59 PM, Justin A. Lemkul wrote: > > > Dr. Vitaly V. Chaban wrote: >> >> Hello Juliette: >> >> If you observe such behavior, I would suggest just to decrease a >> time-step. You should have the same energies at all temperatures. >> >> The larger is a time-step, the larger is a deviation from the energy >> minimum (bonded potentials). The larger is the deviation, the higher >> energy/force arises in order to get back to the equilibrium. >> >> > > Shorter time steps may be necessary to maintain stability of the system and > to conserve energy, certainly, but I don't understand your point about the > energy being independent of temperature. Increasing temperature should, in > theory, lead to excited states for bonds so they should be of higher energy. > For NVE, temperature fluctuations and compensatory potential changes keep > the energy constant, but at different temperatures, NVT and NPT ensembles > will inherently have different energies (and techniques like REMD derive > their usefulness in part from this fact). > > A given system should have a constant total energy, but I would certainly > expect a system run at 300 K to have a different total energy from one at > 400 K. > > -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/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] Re: energy terms vs. temperature
Hello Juliette: If you observe such behavior, I would suggest just to decrease a time-step. You should have the same energies at all temperatures. The larger is a time-step, the larger is a deviation from the energy minimum (bonded potentials). The larger is the deviation, the higher energy/force arises in order to get back to the equilibrium. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA > Dear users, > > I have a short question about temperature dependence of enregy terms i.e > bonds, angles, torsions, vdw , electorstatics. I am curious why these > energies increase with T. Especially bonded terms that have no temperature > dependence in the functional form ( force constants), why all bonded energy > terms are increasing with T? > > Thanks for you comments, > J. -- 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] Re: Non-zero total charge
> Hi, > > > My system had a no zero total charge: > System has non-zero total charge: 6.30e+01 > I used genion to neutralize the system by adding 6 CL ions. > > After updating the topology file, the system still seems to have the same > problem. > > It still has a non-zero total charge: > System has non-zero total charge: 5.70e+01 > 63 non-compensated ions in the single system... I wonder what this system is -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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
Re: [gmx-users] Re: which charge is used in gromacs program
On Wed, Aug 31, 2011 at 8:23 PM, Justin A. Lemkul wrote: > > > Dr. Vitaly V. Chaban wrote: >>> >>> Hi, ALL >>> >>> I have a question about the charge defined in the topology file. >>> It seems to me that the charge for each atom apprears twice in >>> different sections of the topology files. >>> >>> -- >>> One is >>> [ atomtypes ] >>> ;name mass charge ptype c6 c12 >>> >>> The other is >>> [ atoms ] >>> ; id at type res nr residu name at name cg nr charge >>> >>> -- >>> And the charge number in [ atomtypes ] are always 0.0. >>> Which one is actually read by gromacs program ? >> >> >> That one which is mentioned the last >> > > That is true in the case where grompp finds multiply defined types for > bonded interactions and atom types; the charges in ffnonbonded.itp are never > used by any program. The reason for their existence is not clear, but > perhaps they were used by older versions or were intended for some > streamlined force field organization that never came to fruition. > I believe, this column is intended for aminoacids for which there should be a consistent set of parameters including charges. This is what we have in AMBER. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: which charge is used in gromacs program
> > Hi, ALL > > I have a question about the charge defined in the topology file. > It seems to me that the charge for each atom apprears twice in > different sections of the topology files. > -- > One is > [ atomtypes ] > ;name mass charge ptype c6 c12 > > The other is > [ atoms ] > ; id at type res nr residu name at name cg nr charge > -- > And the charge number in [ atomtypes ] are always 0.0. > Which one is actually read by gromacs program ? That one which is mentioned the last -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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
Re: [gmx-users] Re: LJ
>Thank you so much for your explanation. I am just guessing in the last >statement you meant *inter* molecular! Yes. INTERmolecular, between chemically nonbonded particles. >> >> Formally, you can kill this energy by going to the main topology file >> (like ffgmx.itp) and setting FudgeLJ term to zero, although I think >> that you don't actually want to do so. LJ-14 is the energy between the >> atoms belonging to the SAME molecule, so if you consider e.g. heat of >> vaporization, cohesive energy density, internal energy (U), you can >> just ignore this term. >> >> If I recollect correctly, nexcl and 1-4 interactions work >> independently. "nexcl" requests to treat the atoms as if they belong >> to separate molecules provided that these two atoms are separated by >> more than a specified number of chemical bonds. 1-4 interactions only >> treat 1-4 atoms using a scaling factor from FudgeLJ (above). >> >> When calculating some intramolecular property, you usually need to use >> only the following terms > > I assume you mean intermolecular here? > >> LJ-(SR) Disper.-corr. Coulomb-(SR) Coul.-recip. >> > > There may be others, depending on the way in which the .mdp file was set, > including LR terms for both LJ and Coulomb. The PME term is not trivially > decomposed, but that's been discussed to death in previous messages. There > may be other terms if PME was not used. Of course. These four are just an example for the most traditional setup for periodic boxes with electrostatics. >> >> >> >> >> On Fri, Aug 26, 2011 at 3:12 PM, Juliette N. >> wrote: >>> >>> On 26 August 2011 13:25, Dr. Vitaly V. Chaban wrote: >>>>>> >>>>>> . Now it is clear that >>>>>> the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded potentials. >>>>>> Thank >>>>>> you so much. >>>> >>>> The answer actually depends on what you call "nonbonded potential". If >>>> you want to calculate e.g. the interaction energy between two >>>> molecules, then you should NOT include this term. >>> >>> Thank you for you reply. I am actually interested in interaction energies >>> (cohesive energy between particles which is related to enthalpy of >>> vaporization) and noticed that inclusion of this term results in far less >>> accurate results. The net energy is of repulsion type and adding a >>> positive >>> term ( LJ-1-4) makes my results inaccurate. I am already using nexcl = 3 >>> in >>> the topology which means 1-5, 1-6 neighbors are accounted for. But still >>> LJ >>> -1-4 is appearing. So far I have been ignoring this term (energy value) >>> in >>> my calculations, but my concern is that by just neglecting this energy >>> term >>> (value) I am not ignoring the actual effect of a potential term on the >>> physics of the system. Is there any way to switch off this term? >>> >>> Thanks, >>>> >>>> -- >>>> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. >>>> Univ. Rochester, Rochester, New York 14627-0216 >>>> THE UNITED STATES OF AMERICA >>>> -- >>>> 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/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 >>> >>> >>> -- >>> Thanks, >>> J. N. >>> >>> > > -- > > > 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 > > > -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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
Re: [gmx-users] Re: LJ
Hi Juliette, Formally, you can kill this energy by going to the main topology file (like ffgmx.itp) and setting FudgeLJ term to zero, although I think that you don't actually want to do so. LJ-14 is the energy between the atoms belonging to the SAME molecule, so if you consider e.g. heat of vaporization, cohesive energy density, internal energy (U), you can just ignore this term. If I recollect correctly, nexcl and 1-4 interactions work independently. "nexcl" requests to treat the atoms as if they belong to separate molecules provided that these two atoms are separated by more than a specified number of chemical bonds. 1-4 interactions only treat 1-4 atoms using a scaling factor from FudgeLJ (above). When calculating some intramolecular property, you usually need to use only the following terms LJ-(SR) Disper.-corr.Coulomb-(SR) Coul.-recip. Vitaly On Fri, Aug 26, 2011 at 3:12 PM, Juliette N. wrote: > > > On 26 August 2011 13:25, Dr. Vitaly V. Chaban wrote: >> >> >>. Now it is clear that >> >> the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded potentials. >> >> Thank >> >> you so much. >> >> The answer actually depends on what you call "nonbonded potential". If >> you want to calculate e.g. the interaction energy between two >> molecules, then you should NOT include this term. > > Thank you for you reply. I am actually interested in interaction energies > (cohesive energy between particles which is related to enthalpy of > vaporization) and noticed that inclusion of this term results in far less > accurate results. The net energy is of repulsion type and adding a positive > term ( LJ-1-4) makes my results inaccurate. I am already using nexcl = 3 in > the topology which means 1-5, 1-6 neighbors are accounted for. But still LJ > -1-4 is appearing. So far I have been ignoring this term (energy value) in > my calculations, but my concern is that by just neglecting this energy term > (value) I am not ignoring the actual effect of a potential term on the > physics of the system. Is there any way to switch off this term? > > Thanks, >> >> -- >> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. >> Univ. Rochester, Rochester, New York 14627-0216 >> THE UNITED STATES OF AMERICA >> -- >> 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/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 > > > > -- > Thanks, > J. N. > > -- 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] Re: LJ
>>. Now it is clear that >> the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded potentials. Thank >> you so much. The answer actually depends on what you call "nonbonded potential". If you want to calculate e.g. the interaction energy between two molecules, then you should NOT include this term. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: LJ
>> >>> Hello everyone, >>> >>> I know the following question has been discussed many times in the archive >>> but unfortunately I am still unclear about it therefore I would like to ask >>> for your patience. >>> >>> I am interested in non bonded interactions, i.e LJ(SR) and it has been >>> said that LJ-14 potentials are /inter/molecular non bonded interactions. >>> >> >> 1-4 interactions are intramolecular, occurring between atoms separated by 3 >> bonds. They are not intermolecular. > > > Sorry, that was my mistake. I meant intra/ molecular nonbonded. Thats is why > I was wondering if I have to add up to LJ SR or not. Now it is clear that > the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded potentials. Thank > you so much. I guess they are non-bonded because these atoms are not directly bound. They are separated by 3 chemical bonds, yet belonging to the same molecule. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] postdoc positions in chemical physics
Hi all, Just to inform you about the new openings in our team. = August 2011 POSTDOCTORAL SCHOLAR POSITIONS THEORETICAL AND COMPUTATIONAL CHEMICAL PHYSICS Postdoctoral positions are immediately available in the theory group of Professor Oleg Prezhdo. (A) Excited State Dynamics in Nanoscale Materials. Time-domain, atomistic simulation of excitation and electron transfer, electron-phonon relaxation, spin dynamics and related processes on nanoscale, including molecule-bulk interfaces, semiconducting and metallic quantum dots, carbon nanotubes and graphene nanoribbons, as motivated by photovoltaics, molecular electronics, spintronics, ultrafast spectroscopies, DNA sequencing, laser therapies, etc. (B) Non-Adiabatic Molecular Dynamics and Time-Dependent Density Functional Theory. Development and implementation of NAMD and TDDFT algorithms with the aim at the applications described in (A). Fundamental aspects of semiclassical physics, coupling of quantum and classical (or semiclassical) dynamics, system-bath interactions. Interested candidates should submit their CVs, including a list of references to oleg.prez...@rochester.edu 1. S. A. Fischer, C. M. Isborn, O. V. Prezhdo, “Excited states and optical absorption of small semiconducting clusters: dopants, defects and charging”, Chem. Science, 2, 400 (2011). 2. O. V. Prezhdo “Photoinduced dynamics in semiconductor quantum dots: insights from time-domain ab initio studies”, Acc. Chem. Res., 42, 2005 (2009). 3. O. V. Prezhdo, W. R. Duncan, V. V. Prezhdo, “Dynamics of the photoexcited electron at the chromophoresemiconductor interface”, Acc. Chem. Res., 41, 339 (2008). 4. O. V. Prezhdo, “Quantized Hamilton dynamics”, Theor. Chem. Acc., vol. "New Perspectives in Theoretical Chemistry", 116, 206 (2006). 5. C. F. Craig, W. R. Duncan, O. V. Prezhdo “Trajectory surface hopping in the time-dependent Kohn-Sham theory for electron-nuclear dynamics”, Phys. Rev. Lett., 95 163001 (2005) === -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: parallel job crash for large system
>> Does a different barostat work? No. Switching to Berendsen barostat did not help. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: parallel job crash for large system
On Mon, Aug 22, 2011 at 9:02 PM, Dr. Vitaly V. Chaban wrote: >> Your density seems to be about 70% of what I would expect. Are you >> sure that this is not just a normal case of a poorly equilibrated >> system crashing? That matches with what you say about the density >> growing (although perhaps it has more to do with poor equilibration >> than with mixing, as you suggest)? The density should grow, that's the subject of study. The subsystems are equilibrated separately. Again, the crash occurs only after several hundreds thousands of steps. Bad geometries die during the first ps. > >> In any event, I'd suggest simplifying your system and making it >> smaller to see of you can reproduce the problem with a system that >> will run quickly in serial. The bad thing is that it works with smaller, however, not so "long" system... Actually I am sure that the problem is *NOT* in my input molecular configuration. But it is interesting where it is anyway. Interestingly, if I retrieve the last configuration before crash from the TRAJ.XTC and start from it, initializing velocities again, it passes the old crash point. If I start from checkpoint, it crashes. Vitaly > > >> On 23/08/2011 8:44 AM, Dr. Vitaly V. Chaban wrote: >>> In the below issue, the barostat is setup semiisotropically and works >>> only along the "long" direction. The density of the system slowly >>> grows due to mixing. If this can be useful.... >> >> Does a different barostat work? >> >> Mark >> >>> >>> >>> On Mon, Aug 22, 2011 at 5:32 PM, Dr. Vitaly V. Chaban >>> wrote: >>>> We are running the system consisting of 84000 atoms in >>>> parallelepipedic box, 6x6x33nm. The starting geometry, etc are OK and >>>> evolution of trajectory is reasonable but after several hundred >>>> thousands of steps it suddenly crashes. Mysteriously, each time it >>>> crashes at different time-steps, but it always occurs. The parts of >>>> this system were equilibrated separately and did not crash. The system >>>> is not in equilibrium but without external forces. The >>>> Parrinello-Rahman barostat is turned on. The md.log does not show any >>>> problems, the PDB configurations are not written down before crash, >>>> the constaints are absent, the time-step is 1fs that is OK for >>>> separate components (in separate boxes). >>>> >>>> With serial gromacs, the error is not yet observed, but given the size >>>> the run is very slow. >>>> >>>> What can it be? Can it be somehow connected with the very (oblongated) box? > -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: parallel job crash for large system
> Your density seems to be about 70% of what I would expect. Are you > sure that this is not just a normal case of a poorly equilibrated > system crashing? That matches with what you say about the density > growing (although perhaps it has more to do with poor equilibration > than with mixing, as you suggest)? The density should grow, that's the subject of study. The subsystems are equilibrated separately. Again, the crash occurs only after several hundreds thousands of steps. Bad geometries die during the first ps. > In any event, I'd suggest simplifying your system and making it > smaller to see of you can reproduce the problem with a system that > will run quickly in serial. The bad thing is that it works with smaller, however, not so "long" system... Actually I am sure that the problem is in my input molecular configuration. But it is interesting where it is anyway. Interestingly, if I retrieve the last configuration before crash from the TRAJ.XTC and start from it, initializing velocities again, it passes the old crash point. If I start from checkpoint, it crashes. Vitaly > On 23/08/2011 8:44 AM, Dr. Vitaly V. Chaban wrote: >> In the below issue, the barostat is setup semiisotropically and works >> only along the "long" direction. The density of the system slowly >> grows due to mixing. If this can be useful > > Does a different barostat work? > > Mark > >> >> >> On Mon, Aug 22, 2011 at 5:32 PM, Dr. Vitaly V. Chaban >> wrote: >>> We are running the system consisting of 84000 atoms in >>> parallelepipedic box, 6x6x33nm. The starting geometry, etc are OK and >>> evolution of trajectory is reasonable but after several hundred >>> thousands of steps it suddenly crashes. Mysteriously, each time it >>> crashes at different time-steps, but it always occurs. The parts of >>> this system were equilibrated separately and did not crash. The system >>> is not in equilibrium but without external forces. The >>> Parrinello-Rahman barostat is turned on. The md.log does not show any >>> problems, the PDB configurations are not written down before crash, >>> the constaints are absent, the time-step is 1fs that is OK for >>> separate components (in separate boxes). >>> >>> With serial gromacs, the error is not yet observed, but given the size >>> the run is very slow. >>> >>> What can it be? Can it be somehow connected with the very (oblongated) box? -- 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] Re: parallel job crash for large system
> > On 23/08/2011 8:44 AM, Dr. Vitaly V. Chaban wrote: >> In the below issue, the barostat is setup semiisotropically and works >> only along the "long" direction. The density of the system slowly >> grows due to mixing. If this can be useful > > Does a different barostat work? No idea. Should try. Do you think it is a barostat issue? There were two systems on the first stage, ~6x6x8nm and ~6x6x22nm. They were OK, also with semiisotropic pressure coupling. Then the boxes were merged, so that the interface of two liquids forms. Again, after several hundreds of ps (not fs!) of this interface simulation there are no problems and then suddenly error occurs. Of course, I am pretty sure about the force fields, starting configuration, etc, etc... Vitaly >> On Mon, Aug 22, 2011 at 5:32 PM, Dr. Vitaly V. Chaban >> wrote: >>> We are running the system consisting of 84000 atoms in >>> parallelepipedic box, 6x6x33nm. The starting geometry, etc are OK and >>> evolution of trajectory is reasonable but after several hundred >>> thousands of steps it suddenly crashes. Mysteriously, each time it >>> crashes at different time-steps, but it always occurs. The parts of >>> this system were equilibrated separately and did not crash. The system >>> is not in equilibrium but without external forces. The >>> Parrinello-Rahman barostat is turned on. The md.log does not show any >>> problems, the PDB configurations are not written down before crash, >>> the constaints are absent, the time-step is 1fs that is OK for >>> separate components (in separate boxes). >>> >>> With serial gromacs, the error is not yet observed, but given the size >>> the run is very slow. >>> >>> What can it be? Can it be somehow connected with the very (oblongated) box? >>> >>> -- 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] Re: parallel job crash for large system
In the below issue, the barostat is setup semiisotropically and works only along the "long" direction. The density of the system slowly grows due to mixing. If this can be useful On Mon, Aug 22, 2011 at 5:32 PM, Dr. Vitaly V. Chaban wrote: > We are running the system consisting of 84000 atoms in > parallelepipedic box, 6x6x33nm. The starting geometry, etc are OK and > evolution of trajectory is reasonable but after several hundred > thousands of steps it suddenly crashes. Mysteriously, each time it > crashes at different time-steps, but it always occurs. The parts of > this system were equilibrated separately and did not crash. The system > is not in equilibrium but without external forces. The > Parrinello-Rahman barostat is turned on. The md.log does not show any > problems, the PDB configurations are not written down before crash, > the constaints are absent, the time-step is 1fs that is OK for > separate components (in separate boxes). > > With serial gromacs, the error is not yet observed, but given the size > the run is very slow. > > What can it be? Can it be somehow connected with the very (oblongated) box? > > > Stdout below: > > 5000 steps, 5.0 ps. > [exciton04:10256] *** Process received signal *** > [exciton04:10256] Signal: Segmentation fault (11) > [exciton04:10256] Signal code: Address not mapped (1) > [exciton04:10256] Failing at address: 0x6c0ebf10 > [exciton04:10257] *** Process received signal *** > [exciton04:10257] Signal: Segmentation fault (11) > [exciton04:10257] Signal code: Address not mapped (1) > [exciton04:10257] Failing at address: 0x6378320 > [exciton04:10253] *** Process received signal *** > [exciton04:10253] Signal: Segmentation fault (11) > [exciton04:10253] Signal code: Address not mapped (1) > [exciton04:10253] Failing at address: 0x1bfbe110 > [exciton04:10253] [ 0] /lib64/libpthread.so.0 [0x3402a0eb10] > [exciton04:10253] [ 1] mdrun [0x66bb4d] > [exciton04:10253] *** End of error message *** > [exciton04:10255] *** Process received signal *** > [exciton04:10255] Signal: Segmentation fault (11) > [exciton04:10255] Signal code: Address not mapped (1) > [exciton04:10255] Failing at address: 0x13dd139b0 > [exciton04:10255] [ 0] /lib64/libpthread.so.0 [0x3402a0eb10] > [exciton04:10255] [ 1] mdrun [0x66bb5e] > [exciton04:10255] *** End of error message *** > [exciton04:10256] [ 0] /lib64/libpthread.so.0 [0x3402a0eb10] > [exciton04:10256] [ 1] mdrun [0x66bb6f] > [exciton04:10256] *** End of error message *** > [exciton04:10254] *** Process received signal *** > [exciton04:10254] Signal: Segmentation fault (11) > [exciton04:10254] Signal code: Address not mapped (1) > [exciton04:10254] Failing at address: 0x13d2103b0 > [exciton04:10254] [ 0] /lib64/libpthread.so.0 [0x3402a0eb10] > [exciton04:10254] [ 1] mdrun [0x66bb5e] > [exciton04:10254] *** End of error message *** > [exciton04:10257] [ 0] /lib64/libpthread.so.0 [0x3402a0eb10] > [exciton04:10257] [ 1] mdrun [0x66bb5e] > [exciton04:10257] *** End of error message *** > -- > mpirun noticed that process rank 0 with PID 10253 on node exciton04 > exited on signal 11 (Segmentation fault). > ---------- > 5 total processes killed (some possibly by mpirun during cleanup) > > > > The version is 4.0.7 used with OpenMPI. > > -- > Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. > Univ. Rochester, Rochester, New York 14627-0216 > THE UNITED STATES OF AMERICA > -- 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] parallel job crash for large system
We are running the system consisting of 84000 atoms in parallelepipedic box, 6x6x33nm. The starting geometry, etc are OK and evolution of trajectory is reasonable but after several hundred thousands of steps it suddenly crashes. Mysteriously, each time it crashes at different time-steps, but it always occurs. The parts of this system were equilibrated separately and did not crash. The system is not in equilibrium but without external forces. The Parrinello-Rahman barostat is turned on. The md.log does not show any problems, the PDB configurations are not written down before crash, the constaints are absent, the time-step is 1fs that is OK for separate components (in separate boxes). With serial gromacs, the error is not yet observed, but given the size the run is very slow. What can it be? Can it be somehow connected with the very (oblongated) box? Stdout below: 5000 steps, 5.0 ps. [exciton04:10256] *** Process received signal *** [exciton04:10256] Signal: Segmentation fault (11) [exciton04:10256] Signal code: Address not mapped (1) [exciton04:10256] Failing at address: 0x6c0ebf10 [exciton04:10257] *** Process received signal *** [exciton04:10257] Signal: Segmentation fault (11) [exciton04:10257] Signal code: Address not mapped (1) [exciton04:10257] Failing at address: 0x6378320 [exciton04:10253] *** Process received signal *** [exciton04:10253] Signal: Segmentation fault (11) [exciton04:10253] Signal code: Address not mapped (1) [exciton04:10253] Failing at address: 0x1bfbe110 [exciton04:10253] [ 0] /lib64/libpthread.so.0 [0x3402a0eb10] [exciton04:10253] [ 1] mdrun [0x66bb4d] [exciton04:10253] *** End of error message *** [exciton04:10255] *** Process received signal *** [exciton04:10255] Signal: Segmentation fault (11) [exciton04:10255] Signal code: Address not mapped (1) [exciton04:10255] Failing at address: 0x13dd139b0 [exciton04:10255] [ 0] /lib64/libpthread.so.0 [0x3402a0eb10] [exciton04:10255] [ 1] mdrun [0x66bb5e] [exciton04:10255] *** End of error message *** [exciton04:10256] [ 0] /lib64/libpthread.so.0 [0x3402a0eb10] [exciton04:10256] [ 1] mdrun [0x66bb6f] [exciton04:10256] *** End of error message *** [exciton04:10254] *** Process received signal *** [exciton04:10254] Signal: Segmentation fault (11) [exciton04:10254] Signal code: Address not mapped (1) [exciton04:10254] Failing at address: 0x13d2103b0 [exciton04:10254] [ 0] /lib64/libpthread.so.0 [0x3402a0eb10] [exciton04:10254] [ 1] mdrun [0x66bb5e] [exciton04:10254] *** End of error message *** [exciton04:10257] [ 0] /lib64/libpthread.so.0 [0x3402a0eb10] [exciton04:10257] [ 1] mdrun [0x66bb5e] [exciton04:10257] *** End of error message *** -- mpirun noticed that process rank 0 with PID 10253 on node exciton04 exited on signal 11 (Segmentation fault). -- 5 total processes killed (some possibly by mpirun during cleanup) The version is 4.0.7 used with OpenMPI. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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
Re: [gmx-users] h-bonds constraints
Thanks! That's reasonable. On Fri, Aug 19, 2011 at 2:31 PM, Bogdan Costescu wrote: > On Fri, Aug 19, 2011 at 20:02, Dr. Vitaly V. Chaban > wrote: >> What criterion does the grompp utility use to identify H-atoms when it >> is requested in the MDP file to apply constraints=h-bonds? Thanks. > > Any atom name starting with H or h (so case-insensitive). > > Cheers, > Bogdan > -- 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] h-bonds constraints
What criterion does the grompp utility use to identify H-atoms when it is requested in the MDP file to apply constraints=h-bonds? Thanks. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: berendsen P coupling and fluctuation properties
> Thank you. I am looking at potential energies to calculate vaporization > heat. I wanted to know how the fact that berendsen does not lead to correct > ensemble is affecting total potential energy of the system Nohow. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: RTILs
> > I want to simulate system with 128 ionic liquids (128 cation+128 anion). > > I have made a pdb file with a single ionic liquids ion pairs. > > How can I genrate 128 ion pairs using single ion pair .pdb file. GENCONF -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: Heat of Vaporization
I wonder how you know that your polymer chain in computer is exactly your polymer chain in experiment Of course, the difference of vaporazation enthalpy per mole is to be observed. You may guess, may not guess, but method is not guilty if you may not. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA On Wed, Aug 3, 2011 at 4:37 PM, Elisabeth wrote: > > > On 3 August 2011 15:31, Dr. Vitaly V. Chaban wrote: >> >> On Wed, Aug 3, 2011 at 3:17 PM, Elisabeth wrote: >> > >> > >> > On 2 August 2011 15:29, Dr. Vitaly V. Chaban wrote: >> >> >> >> > >> >> > Hello, >> >> > >> >> > I wanted to know your ideas on calculation of heat of vaporization >> >> > using >> >> > a >> >> > single phase run rather than running two separate simulations for >> >> > liquid >> >> > and >> >> > gas! >> >> > >> >> > 1- Two separate simulations for liquid and gas >> >> > >> >> > DHvap = - + RT >> >> > >> >> > 1a: - <*total* potential of a single chain >> >> > in >> >> > vacu >> >> >> ( bond+angle+torsion + nonbonded interaction of chain with itself) >> >> > >> >> > or >> >> > >> >> > 1b: * - < intra potential of a single chain >> >> > in >> >> > vacu >> >> >> ( bond+angle+torsion) * >> >> > >> >> > 2- Single liquid phase run: (non need to run in vacu) >> >> > >> >> > 2a : DHvap = - < intra molecular potential >> >> > terms in >> >> > liquid phase> (same liquid phase simulation by adding up >> >> > bond+angle+torsion >> >> > terms) >> >> > >> >> > 2a: In other worlds *DHvap= * >> >> > >> >> > In my case the latter definition is giving much more accurate results >> >> > than >> >> > 1a. >> >> > >> >> > I would like to know your idea and comments on methods 1b and 2a. >> >> > >> >> > Appreciate your comments. >> >> > >> >> >> >> What is your system? >> >> >> > system is liquid hydrocarbon polymer and 1a is giving inaccurate values. >> > 2a >> > works far better but it seems not to be a common method. >> >> >> First of all, you should understand which particles exist in the vapor >> phase of your polymer. Notwithstanding the atomistic simulation. If >> this question is answered correctly, any method will provide you a >> decent result. >> >> I don't think that the whole "chains" of this polymer are flying in >> the vapor phase. > > Hello, > > Thanks. I have only one single chain in vauo. pbc = no and cutoff is set to > zero for method 1a. Simulation runs for 20 ns and is equilibrated. > Best, > > -- 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] Re: Heat of Vaporization
On Wed, Aug 3, 2011 at 3:17 PM, Elisabeth wrote: > > > On 2 August 2011 15:29, Dr. Vitaly V. Chaban wrote: >> >> > >> > Hello, >> > >> > I wanted to know your ideas on calculation of heat of vaporization using >> > a >> > single phase run rather than running two separate simulations for liquid >> > and >> > gas! >> > >> > 1- Two separate simulations for liquid and gas >> > >> > DHvap = - + RT >> > >> > 1a: - <*total* potential of a single chain in >> > vacu >> >> ( bond+angle+torsion + nonbonded interaction of chain with itself) >> > >> > or >> > >> > 1b: * - < intra potential of a single chain in >> > vacu >> >> ( bond+angle+torsion) * >> > >> > 2- Single liquid phase run: (non need to run in vacu) >> > >> > 2a : DHvap = - < intra molecular potential >> > terms in >> > liquid phase> (same liquid phase simulation by adding up >> > bond+angle+torsion >> > terms) >> > >> > 2a: In other worlds *DHvap= * >> > >> > In my case the latter definition is giving much more accurate results >> > than >> > 1a. >> > >> > I would like to know your idea and comments on methods 1b and 2a. >> > >> > Appreciate your comments. >> > >> >> What is your system? >> > system is liquid hydrocarbon polymer and 1a is giving inaccurate values. 2a > works far better but it seems not to be a common method. First of all, you should understand which particles exist in the vapor phase of your polymer. Notwithstanding the atomistic simulation. If this question is answered correctly, any method will provide you a decent result. I don't think that the whole "chains" of this polymer are flying in the vapor phase. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: Heat of Vaporization
> > Hello, > > I wanted to know your ideas on calculation of heat of vaporization using a > single phase run rather than running two separate simulations for liquid and > gas! > > 1- Two separate simulations for liquid and gas > > DHvap = - + RT > > 1a: - <*total* potential of a single chain in vacu >> ( bond+angle+torsion + nonbonded interaction of chain with itself) > > or > > 1b: * - < intra potential of a single chain in vacu >> ( bond+angle+torsion) * > > 2- Single liquid phase run: (non need to run in vacu) > > 2a : DHvap = - < intra molecular potential terms in > liquid phase> (same liquid phase simulation by adding up bond+angle+torsion > terms) > > 2a: In other worlds *DHvap= * > > In my case the latter definition is giving much more accurate results than > 1a. > > I would like to know your idea and comments on methods 1b and 2a. > > Appreciate your comments. > What is your system? (1a) is what everyone does. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re:g_velacc
> > I am calculating the velocity autocorrelation function for my > system. I have to calculate the g_velacc for 5 different groups within > system. I have made the index file. > > I have also written .sh script > > g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o > h20-vac.xvg > 24 > g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o > h21-vac.xvg > 25 > g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o > h24-vac.xvg > 26 > > How can I select the group. In the above script 24, 25, 26 are the group > numbers in index file. > As always in linux scripts. g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize << EOF 25 EOF -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: Polarizable water model
8 [ exclusions ] ; iatom excluded from interaction with i 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 #ifdef POSRES ; Restrain the oxygen... [ position_restraints ] ; iatom typefx fy fz 1 1 100 100 100 #endif === -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: Polarizable water model
> Is any polarizable water models are available in ITP format? Or may be I > should prepare .itp from some articles? In recent mail archive I've found > some mentions about SWFLEX-AI model. Also I've found van der Spoel's > article. May be somebody have ready .itp files of some models? > There should be a file with polarizable water topology in the standard topology folder of the gromacs installation. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Re: Fw: properdihedrals
Dear Prema: 1. Do you think my e-mail is an alias for gromacs mailing list, please? I am not sure. 2. What about downloading the manual and referring yourself to the section where topology files are described? Enjoy gromaxing... Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA On Tue, Jun 21, 2011 at 2:05 PM, Prema Awati wrote: > > > *-- Original Message --* > From: prem...@iiserpune.ac.in > To: gmxus...@gromacs.org > Date: Tue, 21 Jun 2011 23:25:51 +0530 (GMT+05:30) > Subject: properdihedrals > > Sir, > I am looking forward for your help to calculate Ryckaert-Belleman's (RB) > coefficients using proper dihedrals.Is there any way to get Fourier > coefficients value from the equation; > Vd (φijkl ) = kφ (1 + cos(nφ - φs )) ; so that I can use it in following > way to get RB coefficients; > > C0 = F2 + 1 (F1 + F3 ) > C1 = 1 (-F1 + 3 F3 ) > C2 = -F2 + 4 F4 > C3 = -2 F3 > C4 = -4 F4 > C5 = 0 > I am referring Gromacs-4.5.3 manual for the above conversion. > Looking for your quick response > Thankyou. > -- 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] Re: 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 ? It seems to be much easier in your case to calculate the needed MD box dimensions by hand and edit your conf.gro (last line). You have mass of the box and you have the desired density, so the volume = mass/density. >> 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? You may use spc216.gro as a starting point for all 3-opint waters. As MD runs, SPC "will become" TIP3P or other one based on the data in ITP topology file. -- Dr. Vitaly Chaban http://chaban.at.ua -- 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: Regarding Error "Atomtype OS not found"
> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp > Generated 837 of the 2346 non-bonded parameter combinations > --- > Program grompp, VERSION 4.0.5 > Source code file: toppush.c, line: 947 > Fatal error: > Atomtype OS not found > > Can anyone help me to solve this problem? > > Any kind of help is highly appreciable. Post your "ff_dum.itp" here. -- Dr. Vitaly Chaban http://chaban.at.ua -- 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] from cpmd to gromacs
Hi all, Does anybody have a script translating CPMD trajectory into gromacs XTC and TRR files? Thanks. 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: How to merge 2 simulation boxes?
>> Hi, everyone >> >> I have two simulations which could run well separately. Now I want to place >> the box of simulation A onto the box of simulation B. What should I do to >> realise that? >> >> I've tried to copy and paste the .gro and .top file together, but there are >> several mistakes in grompp. I wonder if there are some better method to >> merge 2 simulation boxes. You probably have duplicate entries in the topollogy file. Remove the unnecessary ones... -- Dr. Vitaly Chaban http://chaban.at.ua -- 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: Problem with GROMACS, please guide me
Yeah... You are a spammer however. I do not see the command you type. On Thu, Mar 25, 2010 at 7:26 PM, Moeed wrote: > Hello, > > Recently, I have started my PhD at McGill and I am a new user of GROMACS. I > am trying to run x2top command to generate topology file but I am getting > the following error message: > > "Invalid command line argument: > > -f " > > could you please help me with this. > > Thank you, > > > > -- > Moeed Shahamat > Graduate Student (Materials Modeling Research Group) > McGill University- Department of Chemical Engineering > Montreal, Quebec H3A 2B2, Canada > Web:http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php > http://mmrg.chemeng.mcgill.ca/ > -- Dr. Vitaly Chaban http://chaban.at.ua -- 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: cutoff problem
On Thu, Mar 25, 2010 at 12:45 AM, XAvier Periole wrote: > > On Mar 24, 2010, at 10:58 PM, Vitaly V. Chaban wrote: > >>> Hi, >>> >>> I want to test different values of cutoff for vdw. However, in the list >>> someone said cutoff = 0.9 for vdw was used for paramaterizing of >Gromos >>> force field, other values would cause error, and also there was someone >>> saying that cutoff for vdw should be set to 1.4. Can >someone make this >>> question clear? Thanks a lot. >> >> The common rule for all FFs is to set the LJ-cutoff around >> 2.5*sigma(LJ12-6). In fact, you'll get about 0.9 nm for the most >> objects. I see nothing terrible if you use, say, 1.4 nm just because >> the difference will be negligible. > > Where is that coming from? This is so wrong! >From the properties of LJ12-6 curve. >> Just test it. :) > > I've you ever tried that on a lipid bilayer? My interests are a bit shifted from bilayers. What concrete atom pair will cause the problem in your example? > Who could ever say (whatever force field) a vdW cutoff of 0.9/1.4 nm > is no difference? >> >> -- >> 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: cutoff problem
> Hi, > > I want to test different values of cutoff for vdw. However, in the list > someone said cutoff = 0.9 for vdw was used for paramaterizing of >Gromos > force field, other values would cause error, and also there was someone > saying that cutoff for vdw should be set to 1.4. Can >someone make this > question clear? Thanks a lot. The common rule for all FFs is to set the LJ-cutoff around 2.5*sigma(LJ12-6). In fact, you'll get about 0.9 nm for the most objects. I see nothing terrible if you use, say, 1.4 nm just because the difference will be negligible. Just test it. :) -- 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:x2top
Charges... Hmmm... I think you have incorrect data types passed to x2top. Vitaly > > I think the result cannot be trusted because the total charge is 1.2, which > seems impossible. I just used the result calculated by Material Studio and I > used the value of charge on the internal atoms. The atoms in surface have > different charges. I have to change the charge by hand. > > P.S. -pbc or -nopbc is depend on if you will use Periodical Boundary > Condition. My pdb is a SiO2 sphere, so I used -nopbc > > Di Cheng -- 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: Using lennard jones and buckingham terms simultaneously
And how will protein and carbonate interact with one another according to your model? Look towards tabulated potentials - with them you can perform any miracles. :) -- Dr. Vitaly Chaban http://chaban.at.ua > I would like to use gromacs-4 to do a simulation of a small protein in water > and in the presence of calcium carbonate. The potential I have for the > calcium carbonate uses Buckingham terms for the interaction between the > calcium and carbonate ions, while the protein obviously interacts through > Lennard Jones terms. It is my understanding from the manual that it is not > possible to mix these two interaction types and so it is not possible to do > this simulation. Also when I attempted to mix lennard jones and buckingham > terms in a topol.top file grompp complained. > > Is there anyway around this problem? > > Many thanks > Gareth -- 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: x2top
Why the result cannot be trusted? The below warning is always output by x2top if I'm not mistaken. Anyway, this is a good idea to check the topologies before starting MD... :) P.S. Maybe -nopbc should be used instead - I don't remember exactly. Use the option which is not default - that is true. On Tue, Mar 23, 2010 at 3:14 PM, 程迪 wrote: > Many Thanks to Dr. Vitaly Chaban > > I just used the command: > > x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa -nopbc > > And here's the output > > ...gromacs' help info... > Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat > WARNING: masses will be determined based on residue and atom names, > this can deviate from the real mass of the atom type > Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat > Entries in atommass.dat: 178 > WARNING: vdwradii will be determined based on residue and atom names, > this can deviate from the real mass of the atom type > Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat > Entries in vdwradii.dat: 28 > Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat > Entries in dgsolv.dat: 7 > Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat > Entries in electroneg.dat: 71 > Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat > Entries in elements.dat: 218 > Looking whether force field files exist > Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp > Opening library file ffoplsaa.n2t > Opening library file ffoplsaa.n2t > There are 6 name to type translations > Generating bonds from distances... > atom 299 > There are 2 different atom types in your sample > Generating angles and dihedrals from bonds... > Before cleaning: 838 pairs > Before cleaning: 838 dihedrals > There are 312 Ryckaert-Bellemans dihedrals, 0 impropers, 628 angles > 838 pairs, 354 bonds and 299 atoms > Total charge is 1.2, total mass is 6003.98 > > WARNING: topologies generated by x2top can not be trusted at face value. > Please verify atomtypes and charges by comparison to other > topologies. > > gcq#309: "Gabba Gabba Hey!" (The Ramones) > > Seems like it worked :-) > But the result cannot be trusted. > > Di Cheng > > University of Science and Technology of China > Hefei, Anhui Province 230026 > P. R. China > E-mail: chen...@mail.ustc.edu.cn > Tel.: +86-15321055911 > > > > On Tue, Mar 23, 2010 at 8:10 PM, Vitaly V. Chaban > wrote: >> >> Try to use the following: >> x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa -pbc >> >> -- >> Dr. Vitaly Chaban >> http://chaban.at.ua >> >> >> >> >> > >> > Hi, everyone >> > >> > I've just tried x2top. >> > >> > My ffoplsaa.n2t file is as follows >> > >> > ;atom atom_type charge mass neighbor_N neighbor >> > distance >> > O opls_002 -0.3 15.9994 2 SI 0.160 SI >> > 0.160 >> > O opls_002 -0.3 15.9994 1 SI 0.160 >> > SI SI 0.6 28.08 1 O 0.160 >> > SI SI 0.6 28.08 2 O 0.160 O 0.160 >> > SI SI 0.6 28.08 3 O 0.160 O 0.160 O 0.160 >> > SI SI 0.6 28.08 4 O 0.160 O 0.160 O 0.160 >> > O >> > 0.160 >> > >> > I entered the command below: >> > >> > x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa >> > >> > here's my output: >> > >> > chen...@chengdi-desktop:~/Gromacs/sio2$ x2top -f SiO2.pdb -o SiO2.top >> > -name > -- 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: x2top
Try to use the following: x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa -pbc -- Dr. Vitaly Chaban http://chaban.at.ua > > Hi, everyone > > I've just tried x2top. > > My ffoplsaa.n2t file is as follows > > ;atom atom_type charge mass neighbor_N neighbor > distance > O opls_002 -0.3 15.9994 2 SI 0.160 SI > 0.160 > O opls_002 -0.3 15.9994 1 SI 0.160 > SI SI 0.6 28.08 1 O 0.160 > SI SI 0.6 28.08 2 O 0.160 O 0.160 > SI SI 0.6 28.08 3 O 0.160 O 0.160 O 0.160 > SI SI 0.6 28.08 4 O 0.160 O 0.160 O 0.160 O > 0.160 > > I entered the command below: > > x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa > > here's my output: > > chen...@chengdi-desktop:~/Gromacs/sio2$ x2top -f SiO2.pdb -o SiO2.top -name -- 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] gromacs/mopac interface
Hi, Is there any example systems to test gromacs/mopac interface? Thanks. Vitaly -- 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:density vs time
Hi Nisha, I mean the volume of the MD cell for NVT ensemble. How did you obtain it? Just replaced one water with one methane molecule? Anyway, I think your RDF is correct. Vitaly > > What do you mean the value for methane? As in the charges? This is my > topology file and I am using OPLS-AA for methane. > > Include forcefield parameters > #include "ffoplsaa.itp" > > [ moleculetype ] > ; Name nrexcl > Methane 3 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass > typeB chargeB massB > 1 opls_138 1 METH C 1 -0.24 12.011 > ; qtot -0.24 > 2 opls_140 1 METH H1 1 0.06 1.008 > ; qtot -0.18 > 3 opls_140 1 METH H2 1 0.06 1.008 > ; qtot -0.12 > 4 opls_140 1 METH H3 1 0.06 1.008 > ; qtot -0.06 > 5 opls_140 1 METH H4 1 0.06 1.008 > ; qtot 0.54 > > [ bonds ] > ; ai aj funct c0 c1 c2 c3 > 1 2 1 > 1 3 1 > 1 4 1 > 1 5 1 > > [ angles ] > ; ai aj ak funct c0 c1 c2 > c3 > 2 1 3 1 > 2 1 4 1 > 2 1 5 1 > 3 1 4 1 > 3 1 5 1 > 4 1 5 1 > > My RDF does look reasonable and the peaks are okay with the values > published earlier, but because of what I am calculating (i.e. volume), > it seems to be very sensitive and even 0.01 makes a difference. > > Thanks for suggestions. > > -Nisha P > > > Quoting "Vitaly V. Chaban" : > >>> >>> I am trying to get an rdf graph actually, and my values are very close >>> to one, but not exactly one, and I was wondering if there is some >>> normalization issue with g_rdf? These are my values for rdf: >>> >>> >>> >>> >>> Near the end, the values are fluctuating around one. The reason I was >>> trying to get density values was may be to try an understand if the >>> density computed by gromacs is different for just water system and >>> water+one methane system (i.e. gromacs calculates the density using >>> the box and total number of molecules in the box, which would be fine >>> for water system but for methane+water it would slightly be a little >>> different, no?) and may be normalize my rdf using the difference in >>> the density factor. Does that make sense? >>> >>> -Nisha >> >> If you don't use barostat, the density of the system is fixed by >> yourself. g_rdf uses it to calculate the average particle density in >> the box. Your rdf seems very reasonable as for me. >> This is another question how you selected the concrete value for >> methane in water system... >> >> >> -- >> 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: density vs time
> > I am trying to get an rdf graph actually, and my values are very close > to one, but not exactly one, and I was wondering if there is some > normalization issue with g_rdf? These are my values for rdf: > > 0 0 > 0.002 0 > 0.004 0 > 0.006 0 > 0.008 0 > 0.01 0 > 0.012 0 > 0.014 0 > 0.016 0 > 0.018 0 > 0.02 0 > 0.022 0 > 0.024 0 > 0.026 0 > 0.028 0 > 0.03 0 > 0.032 0 > 0.034 0 > 0.036 0 > 0.038 0 > 0.04 0 > 0.042 0 > 0.044 0 > 0.046 0 > 0.048 0 > 0.05 0 > 0.052 0 > 0.054 0 > 0.056 0 > 0.058 0 > 0.06 0 > 0.062 0 > 0.064 0 > 0.066 0 > 0.068 0 > 0.07 0 > 0.072 0 > 0.074 0 > 0.076 0 > 0.078 0 > 0.08 0 > 0.082 0 > 0.084 0 > 0.086 0 > 0.088 0 > 0.09 0 > 0.092 0 > 0.094 0 > 0.096 0 > 0.098 0 > 0.1 0 > 0.102 0 > 0.104 0 > 0.106 0 > 0.108 0 > 0.11 0 > 0.112 0 > 0.114 0 > 0.116 0 > 0.118 0 > 0.12 0 > 0.122 0 > 0.124 0 > 0.126 0 > 0.128 0 > 0.13 0 > 0.132 0 > 0.134 0 > 0.136 0 > 0.138 0 > 0.14 0 > 0.142 0 > 0.144 0 > 0.146 0 > 0.148 0 > 0.15 0 > 0.152 0 > 0.154 0 > 0.156 0 > 0.158 0 > 0.16 0 > 0.162 0 > 0.164 0 > 0.166 0 > 0.168 0 > 0.17 0 > 0.172 0 > 0.174 0 > 0.176 0 > 0.178 0 > 0.18 0 > 0.182 0 > 0.184 0 > 0.186 0 > 0.188 0 > 0.19 0 > 0.192 0 > 0.194 0 > 0.196 0 > 0.198 0 > 0.2 0 > 0.202 0 > 0.204 0 > 0.206 0 > 0.208 0 > 0.21 0 > 0.212 0 > 0.214 0 > 0.216 0 > 0.218 0 > 0.22 0 > 0.222 0 > 0.224 0 > 0.226 0 > 0.228 0 > 0.23 0 > 0.232 0 > 0.234 0 > 0.236 0 > 0.238 0 > 0.24 0 > 0.242 0 > 0.244 0 > 0.246 0 > 0.248 0 > 0.25 0 > 0.252 0 > 0.254 0 > 0.256 0 > 0.258 0 > 0.26 0 > 0.262 0 > 0.264 0 > 0.266 0 > 0.268 3.32195e-05 > 0.27 3.27293e-05 > 0.272 0.000193501 > 0.274 0.000317806 > 0.276 0.000689078 > 0.278 0.00126578 > 0.28 0.00197816 > 0.282 0.00348035 > 0.284 0.00653762 > 0.286 0.038 > 0.288 0.016713 > 0.29 0.0238596 > 0.292 0.0345034 > 0.294 0.0528889 > 0.296 0.0698775 > 0.298 0.0933922 > 0.3 0.118079 > 0.302 0.156417 > 0.304 0.195336 > 0.306 0.242149 > 0.308 0.287833 > 0.31 0.351093 > 0.312 0.411434 > 0.314 0.473243 > 0.316 0.538749 > 0.318 0.61093 > 0.32 0.688108 > 0.322 0.756748 > 0.324 0.837504 > 0.326 0.914596 > 0.328 0.993652 > 0.33 1.0663 > 0.332 1.13958 > 0.334 1.21522 > 0.336 1.29358 > 0.338 1.35543 > 0.34 1.42607 > 0.342 1.49061 > 0.344 1.54496 > 0.346 1.59492 > 0.348 1.64578 > 0.35 1.6887 > 0.352 1.73861 > 0.354 1.7676 > 0.356 1.78996 > 0.358 1.82775 > 0.36 1.83798 > 0.362 1.84435 > 0.364 1.85567 > 0.366 1.86664 > 0.368 1.87024 > 0.37 1.86585 > 0.372 1.85472 > 0.374 1.84964 > 0.376 1.84624 > 0.378 1.82577 > 0.38 1.8069 > 0.382 1.78844 > 0.384 1.77257 > 0.386 1.75025 > 0.388 1.72797 > 0.39 1.69894 > 0.392 1.67908 > 0.394 1.6537 > 0.396 1.62812 > 0.398 1
[gmx-users] Re: diffusion coefficient of oxygen molecule
> Respected experts > I want to calculate the self diffusion cofficient of an oxygen molecule in > water. The experimental value in the literature is found to be 2.5 x 10-9 > nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off > Lennard Jones interaction between water and oxygen. I want to reproduce this > value. In your experience, which model of water would give the closer value. > I have seen that the self diffusion of SPC and TIP4P waters are 3.8 units and > 3.2 units whereas the actual value is 2.4 unit. For oxygen the bonding > potential has been taken to be harmonic. Any knowledge of related literature > would be helpful because I could not find by googling. > > Your idea will really help me. > Neal Many guys enjoy SPCE. Its diffusion constant is lower than those of the models you mentioned, if I'm not mistaken. -- Vitaly V. Chaban, Ph.D. http://www-rmn.univer.kharkov.ua/chaban.html -- 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: gmx-users Digest, Vol 70, Issue 92
> Hi > > what is the best program and force field for md simulation of carbon nano > tubes? There's no such one as for me. -- 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: Fwd: [gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds
Yes, I provided all the possible entries in the N2T.although the problem is the same. I also recreated PDB and re-measured the distances but everything seems pretty correct in my PDB. N N 2 S 0.17 S 0.17 F F 1 C 0.14 S S 4 O 0.17 O 0.17 C 0.18 N 0.17 C C 4 F 0.14 F 0.14 F 0.14 S 0.18 O O 1 S 0.17 Vitaly On Fri, Feb 5, 2010 at 10:13 PM, Justin A. Lemkul wrote: > > > Vitaly V. Chaban wrote: >> >> On Fri, Feb 5, 2010 at 9:13 PM, Justin A. Lemkul wrote: >>> >>> Vitaly V. Chaban wrote: >>>> >>>> In this context, it is interesting how X2TOP decides that two atoms >>>> are connected? Only on the base of N2T: if the atom should have 4 >>>> neighbours, it looks for the appropriate number of them? >>>> >>> That's correct. >> >> >> Then the interesting error is: >> "Fatal error: >> No forcefield type for atom C (1) with 0 bonds" >> >> while PDB contains other atoms than carbon. If it looks for neighbours >> why does not it find them... >> > > The error is complaining that atom 1 (a carbon atom) is not within searching > distance of any atoms to which it should be bonded. Have you specified .n2t > entries for every one of your atoms? For example, it is insufficient to > specify an .n2t line for the central S (in your original post) and expect > x2top to understand that the O, N, and C atoms to which it is connected can > have their atom types determined. You need .n2t entries for all of those > atoms, too, specifying that they are, in turn, connected to S in some way. > The above error suggests that x2top is finding a carbon atom that you have > not defined in the .n2t file. > > -Justin > >> >> >> >>>> In my case, maybe it considers that 0.18 nm is too much for two atoms >>>> to be connected? >>>> >>> The length defined in the .n2t file should be the actual bond length >>> (from >>> the coordinate file) +/- 10%, like specbond.dat, if I recall; x2top >>> should >>> not arbitrarily try to dictate that a bond is too long. >>> >>> -Justin >>> >>>> -- Forwarded message -- >>>> From: Vitaly V. Chaban >>>> Date: Fri, Feb 5, 2010 at 7:56 PM >>>> Subject: Re: [gmx-users] Re: x2top and bonds. No forcefield type for >>>> atom S (2) with 3 bonds >>>> To: jalem...@vt.edu, gmx-users@gromacs.org >>>> >>>> >>>> Yes. This worked even with my N2T. I will probably recreate my PDB... >>>> >>>> >>>> On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul >>>> wrote: >>>>> >>>>> Vitaly V. Chaban wrote: >>>>>> >>>>>> Justin, >>>>>> >>>>>> Am I correct that X2TOP uses only N2T file to make a topology? >>>>>> >>>>> Yes. >>>>> >>>>>> I made the full line for Sulphur but it didn't change the situation. >>>>>> It looks strange that X2TOP notices 3 bonds although I propose to have >>>>>> 4 bonds (and they are present). If I propose 3 bonds, it readily gives >>>>>> an output... This is like it has predefined Sulphur with 3 bonds. >>>>>> >>>>> Certainly not. Take, for example, a simple SO4 molecule: >>>>> >>>>> REMARK >>>>> HETATM 1 OAC DRG 1 5.850 14.800 -12.770 1.00 20.00 >>>>> O >>>>> HETATM 2 SAE DRG 1 4.810 15.780 -12.710 1.00 20.00 >>>>> S >>>>> HETATM 3 OAD DRG 1 3.550 15.150 -12.980 1.00 20.00 >>>>> O >>>>> HETATM 4 OAB DRG 1 4.770 16.390 -11.340 1.00 20.00 >>>>> O >>>>> HETATM 5 OAA DRG 1 5.070 16.850 -13.730 1.00 20.00 >>>>> O >>>>> >>>>> The topology is generated just fine with this .n2t file: >>>>> >>>>> S S 0 32.06 4 O 0.145 O 0.145 O 0.145 O 0.145 >>>>> O OM 0 15.9994 1 S 0.145 >>>>> >>>>> I don't know what might be going on with your system, but I would >>>>> suggest >>>>> creating an .n2t file with only entries pertinent to your system, for >>>>> all >>>>> atoms involved. This is, of course, only really useful for debugging, >>>>> since >
Re: Fwd: [gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds
On Fri, Feb 5, 2010 at 9:13 PM, Justin A. Lemkul wrote: > > > Vitaly V. Chaban wrote: >> >> In this context, it is interesting how X2TOP decides that two atoms >> are connected? Only on the base of N2T: if the atom should have 4 >> neighbours, it looks for the appropriate number of them? >> > > That's correct. Then the interesting error is: "Fatal error: No forcefield type for atom C (1) with 0 bonds" while PDB contains other atoms than carbon. If it looks for neighbours why does not it find them... >> In my case, maybe it considers that 0.18 nm is too much for two atoms >> to be connected? >> > > The length defined in the .n2t file should be the actual bond length (from > the coordinate file) +/- 10%, like specbond.dat, if I recall; x2top should > not arbitrarily try to dictate that a bond is too long. > > -Justin > >> >> -- Forwarded message -- >> From: Vitaly V. Chaban >> Date: Fri, Feb 5, 2010 at 7:56 PM >> Subject: Re: [gmx-users] Re: x2top and bonds. No forcefield type for >> atom S (2) with 3 bonds >> To: jalem...@vt.edu, gmx-users@gromacs.org >> >> >> Yes. This worked even with my N2T. I will probably recreate my PDB... >> >> >> On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul wrote: >>> >>> Vitaly V. Chaban wrote: >>>> >>>> Justin, >>>> >>>> Am I correct that X2TOP uses only N2T file to make a topology? >>>> >>> Yes. >>> >>>> I made the full line for Sulphur but it didn't change the situation. >>>> It looks strange that X2TOP notices 3 bonds although I propose to have >>>> 4 bonds (and they are present). If I propose 3 bonds, it readily gives >>>> an output... This is like it has predefined Sulphur with 3 bonds. >>>> >>> Certainly not. Take, for example, a simple SO4 molecule: >>> >>> REMARK >>> HETATM 1 OAC DRG 1 5.850 14.800 -12.770 1.00 20.00 >>> O >>> HETATM 2 SAE DRG 1 4.810 15.780 -12.710 1.00 20.00 >>> S >>> HETATM 3 OAD DRG 1 3.550 15.150 -12.980 1.00 20.00 >>> O >>> HETATM 4 OAB DRG 1 4.770 16.390 -11.340 1.00 20.00 >>> O >>> HETATM 5 OAA DRG 1 5.070 16.850 -13.730 1.00 20.00 >>> O >>> >>> The topology is generated just fine with this .n2t file: >>> >>> S S 0 32.06 4 O 0.145 O 0.145 O 0.145 O 0.145 >>> O OM 0 15.9994 1 S 0.145 >>> >>> I don't know what might be going on with your system, but I would suggest >>> creating an .n2t file with only entries pertinent to your system, for all >>> atoms involved. This is, of course, only really useful for debugging, >>> since >>> in theory, x2top should be easily extensible by appending the .n2t file. >>> >>> -Justin >>> >>>> Vitaly >>>> >>>> >>>> On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban >>>> wrote: >>>>> >>>>> Hi, >>>>> >>>>> This can be the reason when X2TOP gives the following error: >>>>> " >>>>> Fatal error: >>>>> No forcefield type for atom S (2) with 3 bonds >>>>> " >>>>> ? >>>>> >>>>> I try to translate PDB of the TFSA anion >>>>> O O >>>>> || || >>>>> F3C-S-N-S-CF3 >>>>> || || >>>>> O O >>>>> >>>>> into topology. >>>>> >>>>> >>>>> My PDB contains optimized geometry: >>>>> HEADER TFSA >>>>> COMPND TFSA >>>>> AUTHOR VVC >>>>> ATOM 1 N TFS 1 -0.000 0.444 -0.008 1.00 0.00 >>>>> ATOM 2 S TFS 1 1.401 -0.440 -0.189 1.00 0.00 >>>>> ATOM 3 S TFS 1 -1.400 -0.438 0.189 1.00 0.00 >>>>> ATOM 4 O TFS 1 -1.236 -1.810 -0.833 1.00 0.00 >>>>> ATOM 5 O TFS 1 -1.284 -1.009 1.805 1.00 0.00 >>>>> ATOM 6 O TFS 1 1.293 -1.026 -1.800 1.00 0.00 >>>>> ATOM 7 O TFS 1 1.233 -1.803 0.845 1.00 0.00 >>>>> ATOM 8 C TFS 1 -2.837 0.628 -0.107 1.00 0.00 >>>>> ATOM 9 C TFS
Fwd: [gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds
In this context, it is interesting how X2TOP decides that two atoms are connected? Only on the base of N2T: if the atom should have 4 neighbours, it looks for the appropriate number of them? In my case, maybe it considers that 0.18 nm is too much for two atoms to be connected? -- Forwarded message -- From: Vitaly V. Chaban Date: Fri, Feb 5, 2010 at 7:56 PM Subject: Re: [gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds To: jalem...@vt.edu, gmx-users@gromacs.org Yes. This worked even with my N2T. I will probably recreate my PDB... On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul wrote: > > > Vitaly V. Chaban wrote: >> >> Justin, >> >> Am I correct that X2TOP uses only N2T file to make a topology? >> > > Yes. > >> I made the full line for Sulphur but it didn't change the situation. >> It looks strange that X2TOP notices 3 bonds although I propose to have >> 4 bonds (and they are present). If I propose 3 bonds, it readily gives >> an output... This is like it has predefined Sulphur with 3 bonds. >> > > Certainly not. Take, for example, a simple SO4 molecule: > > REMARK > HETATM 1 OAC DRG 1 5.850 14.800 -12.770 1.00 20.00 > O > HETATM 2 SAE DRG 1 4.810 15.780 -12.710 1.00 20.00 > S > HETATM 3 OAD DRG 1 3.550 15.150 -12.980 1.00 20.00 > O > HETATM 4 OAB DRG 1 4.770 16.390 -11.340 1.00 20.00 > O > HETATM 5 OAA DRG 1 5.070 16.850 -13.730 1.00 20.00 > O > > The topology is generated just fine with this .n2t file: > > S S 0 32.06 4 O 0.145 O 0.145 O 0.145 O 0.145 > O OM 0 15.9994 1 S 0.145 > > I don't know what might be going on with your system, but I would suggest > creating an .n2t file with only entries pertinent to your system, for all > atoms involved. This is, of course, only really useful for debugging, since > in theory, x2top should be easily extensible by appending the .n2t file. > > -Justin > >> Vitaly >> >> >> On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban >> wrote: >>> >>> Hi, >>> >>> This can be the reason when X2TOP gives the following error: >>> " >>> Fatal error: >>> No forcefield type for atom S (2) with 3 bonds >>> " >>> ? >>> >>> I try to translate PDB of the TFSA anion >>> O O >>> || || >>> F3C-S-N-S-CF3 >>> || || >>> O O >>> >>> into topology. >>> >>> >>> My PDB contains optimized geometry: >>> HEADER TFSA >>> COMPND TFSA >>> AUTHOR VVC >>> ATOM 1 N TFS 1 -0.000 0.444 -0.008 1.00 0.00 >>> ATOM 2 S TFS 1 1.401 -0.440 -0.189 1.00 0.00 >>> ATOM 3 S TFS 1 -1.400 -0.438 0.189 1.00 0.00 >>> ATOM 4 O TFS 1 -1.236 -1.810 -0.833 1.00 0.00 >>> ATOM 5 O TFS 1 -1.284 -1.009 1.805 1.00 0.00 >>> ATOM 6 O TFS 1 1.293 -1.026 -1.800 1.00 0.00 >>> ATOM 7 O TFS 1 1.233 -1.803 0.845 1.00 0.00 >>> ATOM 8 C TFS 1 -2.837 0.628 -0.107 1.00 0.00 >>> ATOM 9 C TFS 1 2.836 0.630 0.105 1.00 0.00 >>> ATOM 10 F TFS 1 -3.996 -0.097 0.093 1.00 0.00 >>> ATOM 11 F TFS 1 -2.805 1.094 -1.408 1.00 0.00 >>> ATOM 12 F TFS 1 -2.807 1.698 0.766 1.00 0.00 >>> ATOM 13 F TFS 1 2.802 1.099 1.404 1.00 0.00 >>> ATOM 14 F TFS 1 2.803 1.698 -0.771 1.00 0.00 >>> ATOM 15 F TFS 1 3.996 -0.093 -0.093 1.00 0.00 >>> END >>> >>> and my n2t file is >>> >>> C C 1 C ; CNT Carbon with one bond >>> C C 2 C C : CNT double bonded Carbon >>> O O 1 C ; CARBONYL OXYGEN (C=O) >>> O OM 1 C ; CARBOXYL OXYGEN (CO-) >>> O OA 2 C H ; HYDROXYL OXYGEN (OH) >>> O OW 2 H H ; WATER OXYGEN >>> N N 3 H C C ; PEPTIDE NITROGEN (N OR NH) >>> N NT 3 H H C ; TERMINAL NITROGEN (NH2) >>> N NL 4 C H H H ; TERMINAL NITROGEN (NH3) >>> N NR5 2 C C ; AROMATIC N (5-RING,2 BONDS) >>> N NR5* 3 C C H ; AROMATIC N (5-RING,3 BONDS) >>> N NP 3 C C FE ; PORP
Re: [gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds
Yes. This worked even with my N2T. I will probably recreate my PDB... On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul wrote: > > > Vitaly V. Chaban wrote: >> >> Justin, >> >> Am I correct that X2TOP uses only N2T file to make a topology? >> > > Yes. > >> I made the full line for Sulphur but it didn't change the situation. >> It looks strange that X2TOP notices 3 bonds although I propose to have >> 4 bonds (and they are present). If I propose 3 bonds, it readily gives >> an output... This is like it has predefined Sulphur with 3 bonds. >> > > Certainly not. Take, for example, a simple SO4 molecule: > > REMARK > HETATM 1 OAC DRG 1 5.850 14.800 -12.770 1.00 20.00 > O > HETATM 2 SAE DRG 1 4.810 15.780 -12.710 1.00 20.00 > S > HETATM 3 OAD DRG 1 3.550 15.150 -12.980 1.00 20.00 > O > HETATM 4 OAB DRG 1 4.770 16.390 -11.340 1.00 20.00 > O > HETATM 5 OAA DRG 1 5.070 16.850 -13.730 1.00 20.00 > O > > The topology is generated just fine with this .n2t file: > > S S 0 32.06 4 O 0.145 O 0.145 O 0.145 O 0.145 > O OM 0 15.9994 1 S 0.145 > > I don't know what might be going on with your system, but I would suggest > creating an .n2t file with only entries pertinent to your system, for all > atoms involved. This is, of course, only really useful for debugging, since > in theory, x2top should be easily extensible by appending the .n2t file. > > -Justin > >> Vitaly >> >> >> On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban >> wrote: >>> >>> Hi, >>> >>> This can be the reason when X2TOP gives the following error: >>> " >>> Fatal error: >>> No forcefield type for atom S (2) with 3 bonds >>> " >>> ? >>> >>> I try to translate PDB of the TFSA anion >>> O O >>> || || >>> F3C-S-N-S-CF3 >>> || || >>> O O >>> >>> into topology. >>> >>> >>> My PDB contains optimized geometry: >>> HEADER TFSA >>> COMPND TFSA >>> AUTHOR VVC >>> ATOM 1 N TFS 1 -0.000 0.444 -0.008 1.00 0.00 >>> ATOM 2 S TFS 1 1.401 -0.440 -0.189 1.00 0.00 >>> ATOM 3 S TFS 1 -1.400 -0.438 0.189 1.00 0.00 >>> ATOM 4 O TFS 1 -1.236 -1.810 -0.833 1.00 0.00 >>> ATOM 5 O TFS 1 -1.284 -1.009 1.805 1.00 0.00 >>> ATOM 6 O TFS 1 1.293 -1.026 -1.800 1.00 0.00 >>> ATOM 7 O TFS 1 1.233 -1.803 0.845 1.00 0.00 >>> ATOM 8 C TFS 1 -2.837 0.628 -0.107 1.00 0.00 >>> ATOM 9 C TFS 1 2.836 0.630 0.105 1.00 0.00 >>> ATOM 10 F TFS 1 -3.996 -0.097 0.093 1.00 0.00 >>> ATOM 11 F TFS 1 -2.805 1.094 -1.408 1.00 0.00 >>> ATOM 12 F TFS 1 -2.807 1.698 0.766 1.00 0.00 >>> ATOM 13 F TFS 1 2.802 1.099 1.404 1.00 0.00 >>> ATOM 14 F TFS 1 2.803 1.698 -0.771 1.00 0.00 >>> ATOM 15 F TFS 1 3.996 -0.093 -0.093 1.00 0.00 >>> END >>> >>> and my n2t file is >>> >>> C C 1 C ; CNT Carbon with one bond >>> C C 2 C C : CNT double bonded Carbon >>> O O 1 C ; CARBONYL OXYGEN (C=O) >>> O OM 1 C ; CARBOXYL OXYGEN (CO-) >>> O OA 2 C H ; HYDROXYL OXYGEN (OH) >>> O OW 2 H H ; WATER OXYGEN >>> N N 3 H C C ; PEPTIDE NITROGEN (N OR NH) >>> N NT 3 H H C ; TERMINAL NITROGEN (NH2) >>> N NL 4 C H H H ; TERMINAL NITROGEN (NH3) >>> N NR5 2 C C ; AROMATIC N (5-RING,2 BONDS) >>> N NR5* 3 C C H ; AROMATIC N (5-RING,3 BONDS) >>> N NP 3 C C FE ; PORPHYRIN NITROGEN >>> C C 3 C O * ; BARE CARBON (PEPTIDE,C=O,C-N) >>> ; Note that order is importante here because of wildcards. >>> C C3 4 H H H * ; ALIPHATIC CH3 GROUP >>> C C2 4 H H C * ; ALIPHATIC CH2 GROUP >>> C C1 4 H C * * ; ALIPHATIC CH GROUP >>> C CB 3 C C C ; BARE CARBON (5-,6-RING) >>> H H 1 N ; HYDROGEN BONDED TO NITROGEN >>>
[gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds
Justin, Am I correct that X2TOP uses only N2T file to make a topology? I made the full line for Sulphur but it didn't change the situation. It looks strange that X2TOP notices 3 bonds although I propose to have 4 bonds (and they are present). If I propose 3 bonds, it readily gives an output... This is like it has predefined Sulphur with 3 bonds. Vitaly On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban wrote: > Hi, > > This can be the reason when X2TOP gives the following error: > " > Fatal error: > No forcefield type for atom S (2) with 3 bonds > " > ? > > I try to translate PDB of the TFSA anion > O O > || || > F3C-S-N-S-CF3 > || || > O O > > into topology. > > > My PDB contains optimized geometry: > HEADER TFSA > COMPND TFSA > AUTHOR VVC > ATOM 1 N TFS 1 -0.000 0.444 -0.008 1.00 0.00 > ATOM 2 S TFS 1 1.401 -0.440 -0.189 1.00 0.00 > ATOM 3 S TFS 1 -1.400 -0.438 0.189 1.00 0.00 > ATOM 4 O TFS 1 -1.236 -1.810 -0.833 1.00 0.00 > ATOM 5 O TFS 1 -1.284 -1.009 1.805 1.00 0.00 > ATOM 6 O TFS 1 1.293 -1.026 -1.800 1.00 0.00 > ATOM 7 O TFS 1 1.233 -1.803 0.845 1.00 0.00 > ATOM 8 C TFS 1 -2.837 0.628 -0.107 1.00 0.00 > ATOM 9 C TFS 1 2.836 0.630 0.105 1.00 0.00 > ATOM 10 F TFS 1 -3.996 -0.097 0.093 1.00 0.00 > ATOM 11 F TFS 1 -2.805 1.094 -1.408 1.00 0.00 > ATOM 12 F TFS 1 -2.807 1.698 0.766 1.00 0.00 > ATOM 13 F TFS 1 2.802 1.099 1.404 1.00 0.00 > ATOM 14 F TFS 1 2.803 1.698 -0.771 1.00 0.00 > ATOM 15 F TFS 1 3.996 -0.093 -0.093 1.00 0.00 > END > > and my n2t file is > > C C 1 C ; CNT Carbon with one bond > C C 2 C C : CNT double bonded Carbon > O O 1 C ; CARBONYL OXYGEN (C=O) > O OM 1 C ; CARBOXYL OXYGEN (CO-) > O OA 2 C H ; HYDROXYL OXYGEN (OH) > O OW 2 H H ; WATER OXYGEN > N N 3 H C C ; PEPTIDE NITROGEN (N OR NH) > N NT 3 H H C ; TERMINAL NITROGEN (NH2) > N NL 4 C H H H ; TERMINAL NITROGEN (NH3) > N NR5 2 C C ; AROMATIC N (5-RING,2 BONDS) > N NR5* 3 C C H ; AROMATIC N (5-RING,3 BONDS) > N NP 3 C C FE ; PORPHYRIN NITROGEN > C C 3 C O * ; BARE CARBON (PEPTIDE,C=O,C-N) > ; Note that order is importante here because of wildcards. > C C3 4 H H H * ; ALIPHATIC CH3 GROUP > C C2 4 H H C * ; ALIPHATIC CH2 GROUP > C C1 4 H C * * ; ALIPHATIC CH GROUP > C CB 3 C C C ; BARE CARBON (5-,6-RING) > H H 1 N ; HYDROGEN BONDED TO NITROGEN > H HO 1 O ; HYDROXYL HYDROGEN > H HW 1 OW ; WATER HYDROGEN > H HS 1 S ; HYDROGEN BONDED TO SULFUR > H HC 1 C ; HYDROGEN BONDED TO CARBON > S S 4 C 0.181 N 0.167 O 0.172 O 0.172 > F F 1 C > > > > The Sulphur atoms have each 4 bonds but X2TOP wants them to have only > 3. If I change the string in the N2T to 3 bonds, the topology is > generated but S-C bond is absent. > > What can be the problem? > > Thanks. > -- > Vitaly V. Chaban, Ph.D. > http://www-rmn.univer.kharkov.ua/chaban.html > -- Vitaly V. Chaban, Ph.D. http://www-rmn.univer.kharkov.ua/chaban.html -- 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] x2top and bonds. No forcefield type for atom S (2) with 3 bonds
Hi, This can be the reason when X2TOP gives the following error: " Fatal error: No forcefield type for atom S (2) with 3 bonds " ? I try to translate PDB of the TFSA anion OO || || F3C-S-N-S-CF3 || || OO into topology. My PDB contains optimized geometry: HEADERTFSA COMPNDTFSA AUTHORVVC ATOM 1 N TFS 1 -0.000 0.444 -0.008 1.00 0.00 ATOM 2 S TFS 1 1.401 -0.440 -0.189 1.00 0.00 ATOM 3 S TFS 1 -1.400 -0.438 0.189 1.00 0.00 ATOM 4 O TFS 1 -1.236 -1.810 -0.833 1.00 0.00 ATOM 5 O TFS 1 -1.284 -1.009 1.805 1.00 0.00 ATOM 6 O TFS 1 1.293 -1.026 -1.800 1.00 0.00 ATOM 7 O TFS 1 1.233 -1.803 0.845 1.00 0.00 ATOM 8 C TFS 1 -2.837 0.628 -0.107 1.00 0.00 ATOM 9 C TFS 1 2.836 0.630 0.105 1.00 0.00 ATOM 10 F TFS 1 -3.996 -0.097 0.093 1.00 0.00 ATOM 11 F TFS 1 -2.805 1.094 -1.408 1.00 0.00 ATOM 12 F TFS 1 -2.807 1.698 0.766 1.00 0.00 ATOM 13 F TFS 1 2.802 1.099 1.404 1.00 0.00 ATOM 14 F TFS 1 2.803 1.698 -0.771 1.00 0.00 ATOM 15 F TFS 1 3.996 -0.093 -0.093 1.00 0.00 END and my n2t file is C C 1 C ; CNT Carbon with one bond C C 2 C C : CNT double bonded Carbon O O 1 C ; CARBONYL OXYGEN (C=O) O OM 1 C ; CARBOXYL OXYGEN (CO-) O OA 2 C H ; HYDROXYL OXYGEN (OH) O OW 2 H H ; WATER OXYGEN N N 3 H C C ; PEPTIDE NITROGEN (N OR NH) N NT 3 H H C ; TERMINAL NITROGEN (NH2) N NL 4 C H H H ; TERMINAL NITROGEN (NH3) N NR5 2 C C ; AROMATIC N (5-RING,2 BONDS) N NR5*3 C C H ; AROMATIC N (5-RING,3 BONDS) N NP 3 C C FE ; PORPHYRIN NITROGEN C C 3 C O * ; BARE CARBON (PEPTIDE,C=O,C-N) ; Note that order is importante here because of wildcards. C C3 4 H H H * ; ALIPHATIC CH3 GROUP C C2 4 H H C * ; ALIPHATIC CH2 GROUP C C1 4 H C * * ; ALIPHATIC CH GROUP C CB 3 C C C ; BARE CARBON (5-,6-RING) H H 1 N ; HYDROGEN BONDED TO NITROGEN H HO 1 O ; HYDROXYL HYDROGEN H HW 1 OW ; WATER HYDROGEN H HS 1 S ; HYDROGEN BONDED TO SULFUR H HC 1 C ; HYDROGEN BONDED TO CARBON S S 4 C 0.181 N 0.167 O 0.172 O 0.172 F F 1 C The Sulphur atoms have each 4 bonds but X2TOP wants them to have only 3. If I change the string in the N2T to 3 bonds, the topology is generated but S-C bond is absent. What can be the problem? Thanks. -- Vitaly V. Chaban, Ph.D. http://www-rmn.univer.kharkov.ua/chaban.html -- 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 harmonic bond constant
OK. I found my function type "1" and used k_b in [kJ/mol/nm^2]. Vitaly On Fri, Feb 5, 2010 at 5:39 PM, Erik Marklund wrote: > It depends on the function type. See the table "Intramolecular interaction > definitions" in chapter 5 of the gromacs manual. There you can se the units > associated with the different kinds of interactions. > > Erik > > Vitaly V. Chaban skrev: >> >> Hi, >> >> In what units does gromacs MD engine treats harmonic bond constants? >> In the tutorial, there is a hint about fourth-power potential (related >> to GROMOS-96 FF) which I guess should have a constant in >> [kJ/mol/nm^4], but not in [kJ/mol/nm^2]. Although it seems by the >> absolute value that in the existing FFs (.../top/) including GROMOS96 >> they appear in [kJ/mol/nm^2]. >> >> If the own FF is used, in what units should one type the values of k_b >> in topology file for GROMPP to understand it correctly? My variant is >> [kJ/mol/nm^2]. Please let me know if I'm true. >> >> Thanks. >> > > > -- > --- > Erik Marklund, PhD student > Laboratory of Molecular Biophysics, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys > > -- Vitaly V. Chaban, Ph.D. http://www-rmn.univer.kharkov.ua/chaban.html -- 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] gromacs harmonic bond constant
Hi, In what units does gromacs MD engine treats harmonic bond constants? In the tutorial, there is a hint about fourth-power potential (related to GROMOS-96 FF) which I guess should have a constant in [kJ/mol/nm^4], but not in [kJ/mol/nm^2]. Although it seems by the absolute value that in the existing FFs (.../top/) including GROMOS96 they appear in [kJ/mol/nm^2]. If the own FF is used, in what units should one type the values of k_b in topology file for GROMPP to understand it correctly? My variant is [kJ/mol/nm^2]. Please let me know if I'm true. Thanks. -- Vitaly V. Chaban, Ph.D. http://www-rmn.univer.kharkov.ua/chaban.html -- 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: tutorial for ionic liquid
Hi Catarina, This file contains the parameters for MD run, e.g. timestep, number of steps, etc. Good luck with IL, Vitaly -- Vitaly V. Chaban, Ph.D. http://www-rmn.univer.kharkov.ua/chaban.html On Thu, Feb 4, 2010 at 2:39 PM, Catarina Nunes wrote: > Sorry Vitaly, > Can you tell me what means a file mdp? > Thank you. > Catarina > > Hello Vitaly, > I have a tutorial for ionic liquids of [BMIM] [PF6] but i can´t run it > > > 2010/2/1 Vitaly V. Chaban : >>> Dear all, >>> Do you have any tutorial for ? >>> Best regards >>> Catarina >> >> I have worked with MD of RTILs quite a lot. So if you have got >> concrete questions, you can probably ask me directly. >> >> >> Vitaly V. Chaban, Ph.D. >> http://www-rmn.univer.kharkov.ua/chaban.html >> -- 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: tutorial for ionic liquid
> Dear all, > Do you have any tutorial for ? > Best regards > Catarina I have worked with MD of RTILs quite a lot. So if you have got concrete questions, you can probably ask me directly. Vitaly V. Chaban, Ph.D. http://www-rmn.univer.kharkov.ua/chaban.html -- 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: gmx-users Digest, Vol 69, Issue 129
> > This updating is very infrequent. Usually one sees a value of 5-10 here > (usually 5 for Gromos96). If your neighborlist is updated infrequently, you > can > have problems (poor energy conservation and perhaps incorrect calculation of > interactions). Perhaps this is why your short timestep (0.025 fs) leads to > stability - the neighborlist gets updated every 12.5 fs instead of every 50 > fs. > Usually the neighborlist should be updated every 10-20 fs. > Thanks. This is an interesting idea. I will certainly test it! -- 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: simulation crash with GROMOS96 force field
Please find below === integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 100 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed ;bd-temp = 300 ;bd-fric = 0 ;ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 50 emstep = 0.005 ; Max number of iterations in relax_shells niter= 20 ; Step size (1/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 = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 5000 nstenergy = 2500 ; Output frequency and precisiofor xtc file nstxtcout = 50 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 50 ; 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= 1.45 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field-zero epsilon_rf = 0 rcoulomb-switch = 0 rcoulomb = 1.3 vdw-type = Shift ; cut-off lengths rvdw-switch = 1.1 rvdw = 1.3 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; 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 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = V-rescale ; Groups to couple separately tc-grps =System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 348 ; Pressure coupling Pcoupl = no ;Parrinello-Rahman Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1.0 compressibility = 4.5e-6 ref_p= 1.00 ; Random seed for Andersen thermostat andersen_seed= 815131 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no gen_temp = 298.15 gen_seed = 1993 ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are exclud energygrp_excl = ; NMR refinement stuff ; Distance restraints type: No, Simple or Ensemble disre= No ; Force weighting of pairs in one distance restraint: Conservative or Equal disre-weighting = Conservative ; Use sqrt of the time averaged times the instantaneous violation disre-mixed = no disre-fc = 1000 disre-tau= 0 ; Output frequency for pair distances to energy file nstdisreout = 100 ; Orientation restraints: No or Yes orire= no ; Orientation restraints force constant and tau for time averaging orire-fc = 0 orire-tau= 0 orire-fitgrp = ; Output frequency for trace(SD) to energy file nstorireout = 100 ; Dihedral angle restraints: No, Simple or Ensemble dihre= No dihre-fc = 1000 ; Output frequency for dihedral values to energy file === On Mon, Jan 25, 2010 at 10:27 PM, Justin A. Lemkul wrote: > > > Vitaly V. Chaban wrote: >>> >>> 1. No problem at all in vacuo? That with
[gmx-users] Re: simulation crash with GROMOS96 force field
> 1. No problem at all in vacuo? That with a 1 fs timestep and the sd > integrator? Strange then that your molecule is ok and the water is ok, > but they are unstable together. Perhaps your'e not getting any LJ > interactions (or not correct ones) between your solute and water? That's > where I would focus my efforts if I was you. I suppose it could also be > solute-solute LJ problems... If I switch off electrostatics between CIP and water, the problem disappeared... Maybe it's really worth to use a smaller timestep for this system ... -- 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: simulation crash with GROMOS96 force field
Dear Chris - > 1. put a single solute in a large vacuum box and use the sd > integrator. Can you reproduce the problem? No problem in vacuo found. > 2. Remove the dihedral parameters entirely. Can you reproduce the problem? The problem appeared between carbon and hydrogen 1-4 atoms... Would you advise to remove them from [pairs] section? Vitaly -- 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: gmx-users Digest, Vol 69, Issue 123
> You said before: > > "> > 5. What does your .top look like? (does it list the organic molecule > > > only once in the [ molecules ] section?) > > Only once." > OK. We misunderstood one another. I meant "CIP is mentioned only once" = "one string with CIP molecules number". So this entry was not really duplicated. > Does this mean you have only one solute? Or that you have only one entry for > solute, which you then have multiple molecules of in the system? There > certainly can be confusion if you aren't describing your system clearly. > > The reason for asking is that the problematic atom numbers (which are greater > than 42, as Chris pointed out) would indicate one of two possibilities: > > 1. CIP is present multiple times, and one of those molecules (at least) is > having a problem. YES. I just need to find out why the problem appears. -- 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: simulation crash with GROMOS96 force field
Justin, All the directives are correct. Chris just mistyped saying >>> [ molecules ] >>> CIP 3 instead of [ moleculetype ] CIP 3 that I orginally send him. He can't know how many CIPs I have in my system because I didn't send him this section. :) Vitaly On Sun, Jan 24, 2010 at 8:39 PM, Justin A. Lemkul wrote: > > > Vitaly V. Chaban wrote: >>> >>> There's your problem (although in a different manner than I thought). >>> If you have, for example, 3 solutes, then you should have >>> >>> [ molecules ] >>> CIP 3 >>> >>> -NOT- >>> >>> [ molecules ] >>> CIP 1 >> >> Of course, the number of moleules in .top and .gro files coincides. >> Otherwise, one would have had immediate crash. >> CIP 3 -> [ moleculetype ] ! >> > > [molecules] is a different directive than [moleculetype]. Under > [moleculetype] you find the name of the molecule and the number of > exclusions, not the number of molecules. Do you have only one solute? If > so, then it cannot be the first molecule in the system, given the atom > numbers in the crash you reported before. Is everything in the [molecules] > directive in the same order as your coordinate file? Did grompp give any > atom type mismatch warnings? > > -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] Re: simulation crash with GROMOS96 force field
> > There's your problem (although in a different manner than I thought). > If you have, for example, 3 solutes, then you should have > > [ molecules ] > CIP 3 > > -NOT- > > [ molecules ] > CIP 1 Of course, the number of moleules in .top and .gro files coincides. Otherwise, one would have had immediate crash. CIP 3 -> [ moleculetype ] ! > Although probably we're miscommunicating on this as I can't see how > that could be stable for 500 ps... > > As an aside, can you really put cgnr in non-ascending order? I have no > reason to think that you can not, but since I've never seen it before > it's worth checking. I checked already. It is not a reason. Even if one treats all the molecule as the only charge group, the crash appears. > Also, Why do you have 4 terms for the bonds? .. > and I'm not sure what happens to those other c2/c3. > I do not know also. :) This is just what was generated by X2TOP. I tried to use only one constant instead but it didn't solve the problem. > Quoting "Vitaly V. Chaban" : > >> Hi Chris, >> >>> 1. Is your system is properly minimized >> >> Of course, it is, based on the energy values. >> >>> 2. If you take the output from a 500 ps run with 0.25 fs timestep and >>> start a 1 fs timestep run, is that new run stable? >> >> Unfortunately the new run also crashes. The crash may be at the very >> end while all the run goes well. >> >>> 3. What are atoms 62 and 80? >> These are non-bonded carbon and hydrogen of the same molecule. >> >>> **4. Why is there a 1-4 between atoms 62 and 80 if you have only water >>> and a 42 atom solute? >> >> Because I have a number of solute molecules. >> >>> 5. What does your .top look like? (does it list the organic molecule >>> only once in the [ molecules ] section?) >> >> Only once. >> >>> 6. Do you have a bond or angle with a massive force constant that >>> should indeed necessitate the small timestep for stability? >> >> I think no... It look very strange for me that the run can be OK >> during 500 ps but then unexpectedly crashes with producing PDB files >> and similar messages about 1-4 interactions. Visualizing the dynamics >> I do not notice anything strange - the molecule bends and oscillates >> like any other does. >> >> Thanks, >> Vitaly >> >> P.S. I list the topology generated by X2TOP below. >> >> [ moleculetype ] >> CIP 3 >> >> [ atoms ] >> ; nr type resnr residue atom cgnr charge mass >> 1 C 1 CIP C 9 0.221961 12.01115 >> 2 C 1 CIP C 11 0.055382 12.01115 >> 3 C 1 CIP C 10 -0.089181 12.01115 >> 4 C 1 CIP C 8 -0.194750 12.01115 >> 5 C 1 CIP C 7 -0.130399 12.01115 >> 6 C 1 CIP C 7 -0.041791 12.01115 >> 7 N 1 CIP N 6 0.063498 14.0067 >> 8 C 1 CIP C 3 -0.117160 12.01115 >> 9 C 1 CIP C 3 -0.177274 12.01115 >> 10 C 1 CIP C 2 0.545958 12.01115 >> 11 O 1 CIP O 2 -0.663625 15.9994 >> 12 C 1 CIP C 1 0.656204 12.01115 >> 13 O 1 CIP O 1 -0.574855 15.9994 >> 14 O 1 CIP O 1 -0.631961 15.9994 >> 15 F 1 CIP F 9 -0.243679 12.01115 >> 16 N 1 CIP N 11 -0.111246 14.0067 >> 17 C 1 CIP C 6 0.306136 12.01115 >> 18 C 1 CIP C 4 0.043211 12.01115 >> 19 C 1 CIP C 5 -0.718730 12.01115 >> 20 C 1 CIP C 12 0.055448 12.01115 >> 21 C 1 CIP C 14 0.145614 12.01115 >> 22 N 1 CIP N 15 -0.832260 14.0067 >> 23 C 1 CIP C 16 0.169804 12.01115 >> 24 C 1 CIP C 13 -0.169448 12.01115 >> 25 H 1 CIP H 10 0.034855 1.00797 >> 26 H 1 CIP H 8 0.182392 1.00797 >> 27 H 1 CIP H 3 0.180033 1.00797 >> 28 H
[gmx-users] Re: simulation crash with GROMOS96 force field
Hi Chris, > 1. Is your system is properly minimized Of course, it is, based on the energy values. > 2. If you take the output from a 500 ps run with 0.25 fs timestep and > start a 1 fs timestep run, is that new run stable? Unfortunately the new run also crashes. The crash may be at the very end while all the run goes well. > 3. What are atoms 62 and 80? These are non-bonded carbon and hydrogen of the same molecule. > **4. Why is there a 1-4 between atoms 62 and 80 if you have only water > and a 42 atom solute? Because I have a number of solute molecules. > 5. What does your .top look like? (does it list the organic molecule > only once in the [ molecules ] section?) Only once. > 6. Do you have a bond or angle with a massive force constant that > should indeed necessitate the small timestep for stability? I think no... It look very strange for me that the run can be OK during 500 ps but then unexpectedly crashes with producing PDB files and similar messages about 1-4 interactions. Visualizing the dynamics I do not notice anything strange - the molecule bends and oscillates like any other does. Thanks, Vitaly P.S. I list the topology generated by X2TOP below. [ moleculetype ] CIP 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 C 1CIP C 9 0.221961 12.01115 2 C 1CIP C 11 0.055382 12.01115 3 C 1CIP C 10-0.089181 12.01115 4 C 1CIP C 8-0.194750 12.01115 5 C 1CIP C 7-0.130399 12.01115 6 C 1CIP C 7-0.041791 12.01115 7 N 1CIP N 6 0.063498 14.0067 8 C 1CIP C 3-0.117160 12.01115 9 C 1CIP C 3-0.177274 12.01115 10 C 1CIP C 2 0.545958 12.01115 11 O 1CIP O 2-0.663625 15.9994 12 C 1CIP C 1 0.656204 12.01115 13 O 1CIP O 1-0.574855 15.9994 14 O 1CIP O 1-0.631961 15.9994 15 F 1CIP F 9-0.243679 12.01115 16 N 1CIP N 11-0.111246 14.0067 17 C 1CIP C 6 0.306136 12.01115 18 C 1CIP C 4 0.043211 12.01115 19 C 1CIP C 5-0.718730 12.01115 20 C 1CIP C 12 0.055448 12.01115 21 C 1CIP C 14 0.145614 12.01115 22 N 1CIP N 15-0.832260 14.0067 23 C 1CIP C 16 0.169804 12.01115 24 C 1CIP C 13-0.169448 12.01115 25 H 1CIP H 10 0.034855 1.00797 26 H 1CIP H 8 0.182392 1.00797 27 H 1CIP H 3 0.180033 1.00797 28 H 1CIP H 1 0.434432 1.00797 29 H 1CIP H 6 0.039190 1.00797 30 H 1CIP H 4 0.069751 1.00797 31 H 1CIP H 4 0.065460 1.00797 32 H 1CIP H 5 0.261152 1.00797 33 H 1CIP H 5 0.244063 1.00797 34 H 1CIP H 12 0.065977 1.00797 35 H 1CIP H 12 0.013564 1.00797 36 H 1CIP H 14 0.056687 1.00797 37 H 1CIP H 14 0.054216 1.00797 38 H 1CIP H 15 0.394600 1.00797 39 H 1CIP H 16 0.059893 1.00797 40 H 1CIP H 16 0.036976 1.00797 41 H 1CIP H 13 0.109269 1.00797 42 H 1CIP H 13 0.130633 1.00797 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 1 4 1 1.36e-01 4.00e+05 1.36e-01 4.00e+05 115 1 1.33e-01 4.00e+05 1.33e-01 4.00e+05 2 3 1 1.39e-01 4.00e+05 1.39e-01 4.00e+05 216 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 3 6 1 1.39e-01 4.00e+05 1.39e-01 4.00e+05 325 1 1.07e-01 4.00e+05 1.07e-01 4.00e+05 4 5 1 1.39e-01 4.00e+05 1.39e-01 4.00e+05 426 1 1.07e-01 4.00e+05 1.07e-01 4.00e+05 5 6 1 1.40e-01 4.00e+05 1.40
