From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Sun Apr 08 2007 - 13:56:29 CDT
Thanks for the suggestion. I checked and the reference coordinates in my SMDfile exactly match the ones in the *coor file that I use for the restart.
I'm not starting from time zero, but I can't understand exactly what you mean when you say that the coordinates should not match in this case. Is there a reference I can read to understand what you mean?
From: JC Gumbart [mailto:gumbart_at_ks.uiuc.edu]
Sent: Sat 4/7/2007 7:38 PM
To: Ana Celia Araujo Vila Verde
Subject: Re: namd-l: wrong velocity in steered molecular dynamics
Check that the reference coordinates in your SMDfile match those being loaded initially (either coordinates or binCoordinates in case you are restarting from a previous simulation). My bet is that they are very different.
If you are not starting from time 0, then they shouldn't match; instead, the real coordinate should be approximately v*t away from the reference.
On Apr 7, 2007, at 2:29 PM, Ana Celia Araujo Vila Verde wrote:
I'm running a SMD simulation, and I defined SMDVel as 0.00001 (angstroms/timestep). The *log file confirms this velocity: "Info: SMD VELOCITY 1e-05 ANGSTROM/TIMESTEP"
However, during my simulation I find that the SMD atoms travel 38 angstroms in 800 timesteps (0.0475 A/time-step or a whooping 5000 meters/second...)
Can anyone offer some insight as to what is going on?
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:33 CST