Many thanks for your quick reply :) On Tue, Apr 14, 2020 at 11:09 PM Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 4/14/20 4:55 PM, Mohamed Abdelaal wrote: > > Sorry for writing again in the same topic but I couldn't solve > > the velocity problem. > > > > I am trying to reproduce a paper written by: Claire Tonnel + , Martin > > Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, > Alpeshkumar > > K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J. > > Powell > > Title: Elucidating the Spatial Arrangement of Emitter Molecules in > Organic > > Light-Emitting Diode Films > > > > It was mentioned in the paper that " The molecule was inserted into the > > system such that the x and y coordinates of the centre of mass were > sampled > > from a uniform distribution covering the entire box while the z > coordinate > > of the centre of mass was set to 2.0 nm above the current surface. The > > initial orientation of the molecule was randomised. *The velocities of > each > > atom within the inserted molecule in x and y were sampled from a Gaussian > > distribution with a mean of 0.0 nm/ps and a standard deviation > appropriate > > for the temperature constant (σ = sqrt(kT/m), where k B is Botzmann’s , T > > is the temperature and m is the mass of the atom). The velocities in z > were > > sampled from the distribution with the same standard deviation as x and y > > but with a mean of 0.05 nmps -1 , negative z velocities (molecule moving > in > > the direction opposite to the surface) were rectified by taking the > > absolute value. This ensured all molecules moved toward the surface.* > > Presumably the authors used different software; GROMACS does not allow > such granular control of velocities. > > > I have read the section 3.4.1 of the manual version 5.1.2 as recommended > > above and I have also read all the velocity related topics in the manual > > and user guide. > > > > (After Dr. Justin and Dr. Eric replies) I added velocity in my .gro file > > and then I inserted the molecule in a box using insert-molecules, However > > after the insertion process is completed I opened the output .gro file > but > > the velocity was not read. This means that I can only generate the > velocity > > through the .mdp file. > > That's not true. If you know what velocities you want to assign, do so > *after* building the whole system by writing the velocities to the .gro > file (you will need your own code/script to do this). Then do not > generate velocities in the .mdp file and they will be read from the .gro > file. > > > If I am going to generate the velocity using my .mdp file, is it possible > > to change the standard deviation and the mean ? if yes, how can I modify > > them ? (I can't find any way to modify the parameters of the Maxwell > > distribution) > > No, GROMACS has no such capability. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
