Hi Sapna, It is a good question, but such of personal preferences. I found out that my simulations tend to crash more often when I am using 4.5.5. It might be the General-reaction -field I use or something else, I am not sure. Also, it seems I will not gain much from upgrading, so I stick to 4.0.7.
All this is not to say that 4.5.5 is not a good simulation package. It is a good and useful MD package, and I highly appreciate all the time and effort put into it. Best, Itamat PS, there are still people around using 3.3.3 or even 3.2.1, so I am not that behind. On 19/10/2011, at 1:14 PM, Sapna Sarupria wrote: > Dear Itamar, > > Thank you for your response. Why did you prefer to stick to 4.0.7? Is there > something particularly difficult to transfer from 4.0.7 version to 4.5 > version? > > Sapna > > On Tue, Oct 18, 2011 at 9:36 PM, Itamar Kass <itamar.k...@monash.edu> wrote: > Hi Sapna, > > I had the same problem few weeks ago. > > Apparently, some parameters are different (eg. nstpcouple). > > Cheers, > Itamar > > PS I found out that I prefer to stick to 4.0.7. > > > > > On 19/10/2011, at 12:08 PM, Sapna Sarupria wrote: > >> Dear All, >> >> I have a simulation set up for a mixture of carbon dioxide and water system >> which runs perfectly on Gromacs 4.0.5 version. I have run these simulations >> at different temperatures and pressures, from the same starting >> configuration and the simulation proceeds smoothly in the 4.0.5 version. >> However, when I use exactly the same files to run the simulation in 4.5.4 >> version, the system crashes and writes out several pdb files. I was >> wondering if there is anything specific that has been changed between the >> two versions. I have pasted the mdp file of the simulations below. Any input >> will be much appreciated. >> >> MDP File >> >> title = 100% occupancy CO2 hydrate ; a string >> cpp = /lib/cpp ; c-preprocessor >> dt = 0.002 ; time step >> nsteps = 15000000 ; number of steps >> nstcomm = 10 ; reset c.o.m. motion >> nstxout = 0000 ; write coords >> nstvout = 0000 ; write velocities >> nstlog = 25000 ; print to logfile >> nstenergy = 500 ; print energies >> xtc_grps = OW_HW1_HW2_CO2 >> nstxtcout = 1000 >> nstlist = 10 ; update pairlist >> ns_type = grid ; pairlist method >> coulombtype = PME >> rvdw = 1.2 ; cut-off for vdw >> rcoulomb = 1.2 ; cut-off for coulomb >> rlist = 1.2 ; cut-off for coulomb >> DispCorr = EnerPres >> Tcoupl = Nose-Hoover >> ref_t = 270 >> tc-grps = System >> tau_t = 0.5 >> Pcoupl = Parrinello-Rahman >> Pcoupltype = semiisotropic ; pressure geometry >> tau_p = 1.0 1.0 ; p-coupoling time >> compressibility = 4.5e-5 4.5e-5 ; compressibility >> ref_p = 30.5 30.5 ; ref pressure >> gen_vel = yes ; generate initial vel >> gen_temp = 260 ; initial temperature >> gen_seed = 372340 ; random seed >> constraint_algorithm = shake >> constraints = all-bonds >> >> ------- >> >> >> Thank you, >> >> Sincerely, >> Sapna >> -- >> 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 > > ----- > "In theory, there is no difference between theory and practice. But, in > practice, there is." - Jan L.A. van de Snepscheut > > =========================================== > | Itamar Kass, Ph.D. > | Postdoctoral Research Fellow > | > | Department of Biochemistry and Molecular Biology > | Building 77 Clayton Campus > | Wellington Road > | Monash University, > | Victoria 3800 > | Australia > | > | Tel: +61 3 9902 9376 > | Fax: +61 3 9902 9500 > | E-mail: itamar.k...@monash.edu > ============================================ > > > -- > 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 > > > > -- > 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 ----- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut =========================================== | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu ============================================
-- 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