Re: DCD

From: Ernesto Vargas (vargaslo_at_gmail.com)
Date: Thu Apr 05 2012 - 16:21:19 CDT

Hi Maiti,

In TCL you can also use the 'animate' command. One of the options is selection, which you can use to include only the atoms you are interested in.
animate write dcd .....

Ernesto

On Apr 5, 2012, at 4:04 PM, Gianluca Interlandi wrote:

> 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.
> -----------------------------------------------------
>

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