VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Tue Apr 26 2011 - 23:07:07 CDT

Dear John, Axel and Jim,

Thanks for your comments. I have the foll. points to make:

1. There are times when a NAMD job crashes inadvertently (system went down;
not enough disk space; etc). Since the .xsc is written out only at the END
(last step) of the simulation, one would never get it in such cases.
Wouldn't it be great if NAMD offered the option of writing out a
'cumulative' .xsc on the fly?

2. I specifically needed the .xsc for a NAMDenergy calculation with the -PME
option. Can the VMD guys modify the NAMDenergy.tcl script such that the cell
basis can be optionally taken from the .dcd itself (provided, of course,
that the origin is constant and can be provided)?

*I am also copying this message to the vmd mailing list.*

Regards,
Neelanjana

On Tue, Apr 26, 2011 at 10:05 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:

>
> The origin never changes, so it will be the same for any .xsc file for that
> simulation and is probably also in the config file specified with the
> cellOrigin parameter. If you're not using a flexible cell you should be
> able to derive the cell dimensions from the volume and the original cell
> aspect ratio.
>
> -Jim
>
>
>
> On Tue, 26 Apr 2011, Axel Kohlmeyer wrote:
>
> On Tue, 2011-04-26 at 11:02 -0500, John Stone wrote:
>>
>>> Hi,
>>> There's not an existing tool to do this, and I'm not sure that the
>>> associated DCD file and NAMD console output contain enough information
>>> to recreate the lost .xsc file. If the data in the .xsc was redundant
>>>
>>
>> confirmed.
>>
>> the .xsc file in addition contains information about the origin
>> that is not available in a dcd file or VMD.
>>
>> this is the reason why the pbctools have to have a -origin flag.
>> for a periodic simulation the origin is mostly unimportant, but...
>>
>> axel.
>>
>> vs. what's the in DCD file, the .xsc file wouldn't be needed in the first
>>> place.... This question is best asked on the NAMD-L list however, as
>>> the details of your simulation probably matter and either
>>> Jim or the other NAMD experts would know better than I do.
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Wed, Apr 20, 2011 at 05:36:04PM +0530, Neelanjana Sengupta wrote:
>>>
>>>> Dear VMD experts,
>>>>
>>>> While running my simulations with NAMD (mostly with rectangular
>>>> periodic
>>>> boundary conditions), I write out .dcd trajectories that contain the
>>>> unit
>>>> cell information. I usually do not save an .xst file. However, in
>>>> principle, I can write out a file in the format of the corresponding
>>>> .xst
>>>> file.
>>>>
>>>> If (say accidentally) I lose the .xsc file, is there a tool/plugin
>>>> which
>>>> will allow me to generate the .xsc file again, if I am able to provide
>>>> the
>>>> periodic cell parameters?
>>>>
>>>> Thanks in advance,
>>>> Neelanjana Sengupta
>>>>
>>>
>>>
>> --
>> Dr. Axel Kohlmeyer
>> akohlmey_at_gmail.com http://goo.gl/1wk0
>>
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.
>>
>>