From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Apr 05 2012 - 16:30:29 CDT
In general, you don't want to create one huge DCD file. You want to
restart your simulation every certain amount of ns to make sure that your
trajectory is split into several smaller chunks.
The best thing to do now is to use the "animate" command to load only
chunks of your dcd file into VMD:
animate read dcd "yourdcd.dcd" start SSS end EEE waitfor all
Replace SSS and EEE with start and end frames. For example, start with
SSS=0, EEE=999 and then SSS=1000, EEE=1999
In this way, VMD will not freeze your computer. Then you can use Ernesto's
comment with
animate write dcd mydcd_chunk_01.dcd [atomselect top "not (protein or
ions)"]
Gianluca
On Thu, 5 Apr 2012, Buddhadev Maiti wrote:
> Dear Gianluca,
>
> Sorry for my unclear email. My dcd file is very big 30GB and if I try to open, my computer freezes. That is why I am searching some tcl script to strip water and ions. Could you please help me.
> Have a nice day,
> Thanks,
> Maiti
> ________________________________________
> From: Gianluca Interlandi [gianluca_at_u.washington.edu]
> Sent: Thursday, April 05, 2012 5:04 PM
> To: Buddhadev Maiti
> Cc: Jérôme Hénin; namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: DCD
>
> Load your psf+dcd into VMD. Choose File -> Save Coordinates. In the text
> field you can enter your atom selection, e.g., "not (water or ions)"
>
> Gianluca
>
> On Thu, 5 Apr 2012, Buddhadev Maiti wrote:
>
>> Dear Jerome,
>>
>> I would like to make new dcd file from original dcd file (protein +
>> membrane + water + ion) including only protein and membrane part without
>> including any water and ions. Could you please reply me if there is any
>> vmd tcl utilities, it will be great help for me. I am working with psf
>> and dcd files.
>>
>> Have a nice day,
>> Thanks,
>> Maiti
>>
>>
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
>
-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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