VMD-L Mailing List

From: Puspita Halder (puspitah_at_gmail.com)
Date: Fri Jun 27 2014 - 00:35:33 CDT

Hi Maxim,

Thanks for your suggestions. I will definitely try striping out water
molecles from my trajectory file and carry out secondary structure
analysis with the size-reduced file.

Thanks again.
Puspita

On 6/26/14, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
> Hi Puspita,
>
> Getting rid of water greatly speeds up any analysis if/when you don't care
> about water.
>
> It's easy to prepare what you need with VMD and catdcd.
>
> set sel [atomselect top "not water"]
> set out [open "indices_nowater.txt" w]
> puts $out "[$sel list]"
> close $out
> $sel writepsf nowater.psf
>
> catdcd -o nowater.dcd -otype dcd -i indices_nowater.txt trajectory.dcd
>
> At this point, you can load your system without water (mol load psf
> nowater.psf dcd nowater.dcd) and proceed with the proper analysis.
>
> My 30 Gb trajectories shrink to 2 Gb ones and it's much easier to deal with
> them.
>
>
> Maxim
>
>
>
>
> On Jun 26, 2014, at 9:15 AM, Puspita Halder <puspitah_at_gmail.com> wrote:
>
>> Hi,
>>
>> Thanks for your comments. I did not strip out the water molecules of
>> my dcd file. Do u think that would help analyzing the secondary
>> structure of the big dcd file using sscache? I am carrying out other
>> analyses (e.g., rmsd, radius of gyration, sasa etc.) of my large dcd
>> file using bigdcd.tcl. So I was wondering if sscache can be utililized
>> for secondary structure determination of the large dcd file aong with
>> the bigdcd script. Any view on this would be really helpful.
>>
>> Thanks
>> Puspita
>>
>> On 6/26/14, Jeremiah Babcock <zhc605_at_my.utsa.edu> wrote:
>>> Hi Puspita,
>>> Not sure if you did this but if you just need the secondary
>>> structure
>>> of the protein you could strip out the solvent molecules. That would
>>> really
>>> help on the file size. Also, which OS version are you using?
>>>
>>> Regards,
>>> Jeremiah Babcock
>>>
>>>
>>> On Wed, Jun 25, 2014 at 8:23 AM, Puspita Halder <puspitah_at_gmail.com>
>>> wrote:
>>>
>>>> Dear VMD users,
>>>>
>>>> I need to generate the secondary structure of my protein from a 50 ns
>>>> simulation run. I used sscache earlier for 2-4 ns simulations of the
>>>> protein. Now the file sizes are huge (~ 50 GB) so I assume that I
>>>> cannot
>>>> directly use sscache. I tried to combine sscache with bigdcd.tcl script
>>>> but
>>>> failed to do so. Please help me with your valuable suggestions
>>>> regarding
>>>> this. Is there any ready script available ?
>>>>
>>>> Thanks
>>>> Puspita
>>>>
>>>
>
>