From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Apr 05 2012 - 17:04:15 CDT
Sorry, I had a typo. The correct syntax is:
animate read dcd "yourdcd.dcd" beg SSS end EEE waitfor all
So, for example:
animate read dcd file.dcd beg 0 end 999 waitfor all
reads all frames from 0 to 999 of the file "file.dcd". Also, see the VMD
documentation:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node120.html
Gianluca
On Thu, 5 Apr 2012, Gianluca Interlandi wrote:
> 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.
> -----------------------------------------------------
-----------------------------------------------------
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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