[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
