|From:||Axel Kohlmeyer <akohlmey@...24...>|
|Date:||Tue, 14 Nov 2017 13:44:48 -0500|
بسم الله الرحمن الرحيمI have another question about msd compute command:you said in LAMMPS documents "A vector of four quantities is calculated by this compute. The first 3 elements of the vector are the squared dx,dy,dz displacements, summed and averaged over atoms in the group. The 4th element is the total squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the group."Is this the same as calculating the msd for the center of mass of the group of atoms- that used in this command- with time ? I mean this command do the following<(Rcom(t0+t)-Rcom(t0))^2>
and for the time t, Can it be adjusted by a dump command ?
Thank youOn Tue, Nov 14, 2017 at 7:05 PM, A. M.M <alaa.murar@...24...> wrote:بسم االه الرحمن الرحيمThank you.On Tue, Nov 14, 2017 at 7:02 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:On Tue, Nov 14, 2017 at 11:49 AM, A. M.M <alaa.murar@...24...> wrote:بسم الله الرحمن الرحيمI have two questions:1. I used 25 fs for time step, but there are fluctuations in the total energy, Can I neglect it ?this is not a question for this mailing list, but for your adviser (and/or a text book on MD).keep in mind, that you have a *tiny* system, so your ensemble average barely deserves that name.2. I want to dump the total energy of the system with time, I checked the compute command but I do not find a total energy compute command, Is there a way to do that ?I need the structure of dumped file to betime total energyyou can access the total energy through its thermo keyword. how to make use of it (and how to output those), is explained in the manual. please help yourself to another read.axel.Thanks a lot.On Mon, Nov 13, 2017 at 10:47 PM, A. M.M <alaa.murar@...24...> wrote:بسم الله الرحمن الرحيمThanks for your replay and attention Doctor.I will use 25 fs for time step, but there will be a fluctuations in the total energy, Can I neglect it ?I have put my pair coefficients and force constants by myself, and I validate it by calculating the persistance length of it ( because this bead-spring chain represents a dsDNA chain and each bead represents a 6 basepairs of the dsDNA chain), so I change these coefficients and constants until I get the best persistance length at specific salt concentration.Thanks a lot.On Mon, Nov 13, 2017 at 9:04 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:On Mon, Nov 13, 2017 at 1:35 PM, A. M.M <alaa.murar@...24...> wrote:بسم الله الرحمن الرحيمThanks a lot Dr. Kohlmeyer.I did what you said and I got a constant total energy then I turned the thermostat back again but the total energy fluctuates by small values and I can decrees the fluctuations by decreasing the time step more and more but it will be too small. when I use dt=1.0 fmsec the fluctuations of the total energy are small, Can I accept the results now ?a time step of 1fs seems very small for particles as heavy as the ones you have. 1fs is typical with particles of about 15-20 a.u. mass.since typically the maximal time step scales O(sqrt(M)), you should be able to run with at least 15fs timestep, probably even 25fs.when you turn on the langevin thermostat, you'll have some additional damping of fast motions, which might help to get a stable and accurate time integration at a larger time step.the big unknown here is, that your pair coefficients and force constants are different than those for typical atomic systems, so that may also have an impact.but then again, you have such a tiny system, it doesn't really matter that much to use a small timestep.axel.Also, when I used small dt and Tstart=Tstop=298.15 K in fix_langevin, the temperature fluctuates around 298.15 K which I need.Thanks a lot.On Mon, Nov 13, 2017 at 5:23 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:On Mon, Nov 13, 2017 at 10:04 AM, A. M.M <alaa.murar@...24...> wrote:بسم الله الرحمن الرحيمHello,Thanks a lot for your reply.I have attached the inputs file of my system.In the second paragraph, I mean when I put Tstart=Tstop=298.15 K in fix_langevin command I will get a fluctuations around 150-160 K and an ave/time/temp around 150 K, but to get a fluctuations and ave/time/temp around 298.15 K I can increase Tstart and Tstop = 2*298.15 K. Now Can I say that the results of my simulation are in ( ave/time/temp that I get which is around 298.15 K ) or in what I used in fix_langevin command which is 2*298.15 K ?i think you can safely say, that your simulation results are crap.try running without thermostat and check whether you can run a stable simulation that conserves (total) energy.if not, reduce your time step until you can. then turn the thermostat back on and see what happens.axel.Thank youOn Mon, Nov 13, 2017 at 4:08 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:On Sat, Nov 11, 2017 at 11:09 AM, A. M.M <alaa.murar@...24...> wrote:بسم الله الرحمن الرحيمHello LAMMPS user,I used fix_langevin command with fix_nve to perform a BD as mentioned in LAMMPS documents, I put Tstart=Tstop=298.15 K (25 C) and damp = 482 fmsec. Also, I used a time step = 300.0 fmsec, and my system is a 24 bead-spring chain.My simulation run well, but I noticed that the temperature fluctuates below the value that I put in the command, and when I calculate the ave/time/temp I also got around 150-160 K. what is/are the reason/s ?there is not enough information to answer this question. most likely, you are making a mistake somewhere.I can increase the values in the command until I get a fluctuations around 298.15 K and also an ave/time/temp around this value, but now Can I say that the results of mu simulation are in ( ave/time/temp that I get ) or in what I used in the command ?what values in what commands? what exactly are you asking here?good answers require well posed questions with sufficient detail.axel.Thank you
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