Fan, Fenghui wrote:
Dear all,
For MD we need to get a initial velocity of the molecule randomly. Id the velocity linear vvelocity of the whole molecule or the vibration velovcity or some kinds of other velocity?
In addition, as for the molecule is very large, there is the possibility that differeny parts of the protein has different velocity. Does this violate the randomly got velocity?
Further more, for the MD system. it is in fact protein (can include ions and ligands) surrounded by water. Then it seems there will be no linaear movement of the whole molecule.
I am looking forward to having these clarified.
Best regards.
Fenghui Fan
_______________________________________________
gmx-users mailing list gmx-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
this is described in the manual. the velocities are sampled according to
a Maxwell-Boltzmann distribution at the temperature you request.
--
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-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
