Re: Dihedral calculation with colvars

From: Kevin C Chan (
Date: Thu Mar 12 2015 - 06:13:00 CDT

Thanks for the reply!

I understand the fact that wrapping only affects what we load into VMD
after a simulation (coor, dcd, etc.). However my very original question
lies in the inconsistency of my colvar.traj files where I expect the last
line of the previous one should be the same as the first line of the next
one which is not the case.

So do you mean that NAMD reads in a coordinate (either pdb or coor) and do
no wrapping before a simulation? I thought it does or we will have trouble
that feeding a wrapped coor or a unwrapped one would be different.

I will try turning off wrap options in NAMD and try all things again see
whether we will have consistent results.

Thanks in advance,

On Thursday, March 12, 2015, Jérôme Hénin <> wrote:

> Hi Kevin,
> NAMD takes the initial coordinates as they are and starts the simulation
> without wrapping or unwrapping. The colvars use those coordinates. The
> wrapping options only affect output files.
> If you want the output files (DCD and coodinates) to reflect what NAMD
> uses internally, you should disable wrapping. Then you can load that output
> in VMD and calculate the colvars interactively to check their definition.
> Jerome
> On 12 March 2015 at 07:20, Kevin C Chan <
> <javascript:_e(%7B%7D,'cvml','');>> wrote:
>> Thanks for the reply. Sorry that I sent the previous email off-list.
>> No there is no minimisation.
>> I thought about the PBC and I did turn on Wrapall during both simulation--f46d041826b87ebc5c05111577c5--

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