[gmx-users] comm_mode and accelerate
Dear all， To make molecules move, accelerate should be used. nstcomm is the frequency for center of mass motion removal But if they are used together, the molecule will not move. I made a model system: a box of pure water. Adding accelerate to SOL in Z direction. Firstly, comm_mode was set to no. But there was a warning during grompp:"You are not using center of mass motion removal (mdp option comm-mode), numerical rounding errors can lead to build up of kinetic energy of the center of mass。 Net Acceleration in Z direction, will not be corrected" The results really drift. Then nstcomm=10 was set, the averaged velocity of water molecule in Z direction was close to zero. I checked the tpr file using gmxdump, and found out that acc is set to 0, but accelerate = 0.0 0.0 -0.001 is in mdout.mdp, So How to use these two parameter together? Not only make the steady water flow but also not drift? Thanks a lot Candery -- 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] comm_mode
[EMAIL PROTECTED] wrote:
Dear users,
There is an option in .mdp named comm_mode, which deals with the transition
and rotation of the molecule being simulated. I want to know why the transition
and rotation happens during the simulation. Can any one suggest me any
reading material where in I can find how the dynamics is performed internally.
thanks in advance
@Article{Harvey98a,
author = {S. C. Harvey and R. K. Z. Tan and T. E. Cheatham},
title = {The flying ice cube: Velocity rescaling in molecular
dynamics leads to violation of energy equipartition},
journal = {J. Comp. Chem.},
year = 1998,
volume = 19,
pages ={726-740}
}
regards
Anwar
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Mohd Anwaruddin
Project Assistant
C/o DR.H.A.Nagarajaram
Lab of Computational Biology and Bioinformatics
Center for DNA Fingerprinting and Diagnostics(CDFD)
Nacharam
Hyderabad-500 076
INDIA.
Tel: +91-8413-235467,68,69,70 ext 2019
[EMAIL PROTECTED]
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David.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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[gmx-users] comm_mode
Dear users, There is an option in .mdp named comm_mode, which deals with the transition and rotation of the molecule being simulated. I want to know why the transition and rotation happens during the simulation. Can any one suggest me any reading material where in I can find how the dynamics is performed internally. thanks in advance regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
