VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Apr 26 2011 - 23:16:46 CDT

Periodic restart files include .xsc files, and you can also write a .xst
trajectory file, each line of which is the .xsc file for that step.

-Jim

On Wed, 27 Apr 2011, Neelanjana Sengupta wrote:

> 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.
>>>
>>>
>