From: Puspita Halder (
Date: Thu Jun 26 2014 - 09:15:40 CDT


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.


On 6/26/14, Jeremiah Babcock <> 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 <> 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