Re: Restarting MD (Disabling Checklist)

From: Joshua Adelman (
Date: Fri Aug 19 2011 - 07:18:17 CDT

Hi Babban,

On Aug 19, 2011, at 7:50 AM, Babban Mia wrote:

> Can somebody please advise me on this ?.
> Thanks!
> Best
> Babban
> On Thu, Aug 18, 2011 at 9:28 PM, Babban Mia <> wrote:
> While writing a restart config file and using binVelocities ${name}.restart.vel
> What options need to be disabled ?
> Check list :
> temperature 310
> langevinTemp 310
> langevinPistonTemp 310
> reinitvels 310

If you are restarting from a restart velocity, you should not set the `temperature` parameter (but you can use the tcl command `set temperature 310` and then use $temperature to set the other temperature variables where needed), but you will need to specify all of the langevin parameters. You can apply `reinitivels` if you want to randomly reinitialize the velocities, but usually this is not standard between continuous trajectory segments.

> Is there anything more which needs to be disabled ?
> I figured out that even though we load in the coordinates through a <binCoordinates ${name}.restart.coor> restart file. We still need to use the option :
> coordinates ${name}.pdb
> Why is that ?

If you take a look at the manual, it is just a requirement that NAMD specifies:

bincoordinates binary coordinate restart file
Acceptable Values: UNIX filename
Description: The binary restart file containing initial position coordinate data. A binary coordinate restart file is created as output from NAMD by activating the binaryrestart orbinaryoutput options. Note that, in the current implementation at least, the bincoordinates option must be used in addition to the coordinates option, but the positions specified bycoordinates will then be ignored.


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