Hello,
regarding simulations for the diffusion study should one
care about the
nscm flag ( Flag for the removal of translational and rotational
center-of-mass (COM) motion ) ?
---------------------------------------------------------------------------------------
"...For Langevin dynamics, the position of the center-of-mass of the
molecule is reset
to zero every NSCM steps, but the velocities are not affected. ...."
"...The only reason to even reset the coordinates is to prevent the
molecule from diffusing so far away from the origin that its coordinates
overflow the format used in restart or trajectory files. ..."
-----------------------------------------------------------------------------------------
If I understand well this flag is here e.g. to compensate perhaps very
small (especially for bigger systems) but nonzero translational velocity
of the center of mass of the simulation box content as the result of the
random assigning of the initial atom velocities. Am I right ?
Thanks in advance for comments,
Best wishes,
Marek
Dne Tue, 14 Jan 2014 16:55:02 +0100 Daniel Roe <daniel.r.roe.gmail.com>
napsal/-a:
> Hi,
>
> As long as the initial ASCII trajectory is not corrupt (i.e. does not
> contain ****) you can use it with the subsequent NetCDF trajectory
> without
> issue.
>
> -Dan
>
>
> On Tue, Jan 14, 2014 at 8:41 AM, Jio M <jiomm.yahoo.com> wrote:
>
>> Dear Daniel
>>
>> Thanks, one quick question. My earlier simulation upto 50 ns was with
>> iwrap=0 and now I am using netcdf outputs with same iwrap=0. Considering
>> netcdf has much precision; so does that mean I can not "combine" as a
>> regular plot, e.g. some function (say diffusion) vs time, of intial 50ns
>> less precision traj (iwrap=0) with later more precision traj (netcdf).
>>
>> regards
>> J
>>
>>
>>
>>
>> On Tuesday, January 14, 2014 3:32 PM, Daniel Roe
>> <daniel.r.roe.gmail.com>
>> wrote:
>>
>> Hi,
>>
>> You should definitely use NetCDF trajectories since they have better
>> precision and are faster to process. Note that you can also
>> post-process an
>> imaged trajectory with the 'unwrap' command; this will make the
>> trajectory
>> as if you had simulated with iwrap=0.
>>
>> Hope this helps,
>>
>> -Dan
>>
>>
>>
>> On Tue, Jan 14, 2014 at 6:10 AM, Jio M <jiomm.yahoo.com> wrote:
>>
>> Dear All
>> >
>> >My system atoms has diffused very far so getting **** in coordinates.
>> If
>> I am not wrong iwrap=1 put things back in original unit cell. Though I
>> think if I need all track of diffusion then I should use netcdf option
>> (please correct me). I have run just 50 ns and need to go much longer.
>> >
>> >I know only about diffusion analysis which can/should not be performed
>> on
>> trajectories obtained by iwrap=1. Just for future purpose I am curious
>> to
>> know what kind analysis I can NOT perform if I use iwrap=1. But
>> ofcourse I
>> would need to study diffusion things so I should use netcdf format.
>> >
>> >
>> >thanks
>> >Jiom
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>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
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Received on Tue Jan 14 2014 - 09:00:02 PST
