different velocities problem

From: Hasan haska (hasanhaska_at_yahoo.com)
Date: Tue Oct 25 2011 - 01:28:22 CDT

Dear Namd users,   I performed some md simulations for my system adding “velDCDfile†command into the conf file. Then I compared the velocity information for the last record in .vel ascii file and .pdb file generated from the vel.dcd file if velocities are the same. And I realized that velocities of the atoms are different in these two files. What is reason for this ? Can you please make an explanation about this issue ?  In addition to this, when I load vel.dcd into psf file and use “pbc wrap –all†command in vmd then save the velocities for the last record, I got a another different velocity pdb file that has different information. Why these three velocity file has different velocity information ? Which velocities should I take into consideration?  Please see the attached velocity.dat file.   Thanks for your help.

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