Re: DCD

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Apr 05 2012 - 16:27:30 CDT

On Thu, Apr 5, 2012 at 5:22 PM, Buddhadev Maiti <bmaiti_at_gsu.edu> 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.

use catdcd.

please search the mailing list archives for
a more detailed explanations. this topic
comes up regularly.

axel.

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

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.

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