From: Mert Gür (gurmert_at_gmail.com)
Date: Fri Aug 13 2010 - 08:56:44 CDT
Lisa what I would do is the following.
Do your simulations by restarting them so that your dcd file is not
too big to handle it (Less than the RAM of your PC)
Then use the following tcl script in VMD.
for {set i 1} {$i < 20} {incr i} {
mol load psf system.psf
animate read dcd run$i/system.dcd waitfor all
set s1 [atomselect top "protein"]
animate write dcd {protein$i .dcd} waitfor all sel $s1
}
Of course there are other methods to do that, but this is the first
thing that came to me.
Mert
On Fri, Aug 13, 2010 at 4:06 PM, Lisa Brown <lisa.brown2009_at_gmail.com> wrote:
> Thank you Thanassis and Nabil.
> But I need it BEFORE the simulation. I want to do a simulation in a
> solvated system, but I do not need water coordinates in my DCD file at
> all.
> seems to be there's no way .
> anyway thank you for the help.
> Lisa
>
> 2010/8/12 Athanassios Stavrakoudis <astavrak_at_cc.uoi.gr>:
>> Hi Lisa,
>>
>> NAMD will store the coordinates of all atoms.
>> If you want to get rid of the solvent, AFTER the simulation,
>> then Carma or Eucb or catdcd packages might help you:
>> http://utopia.duth.gr/~glykos/carma.html
>> http://stavrakoudis.econ.uoi.gr/eucb
>> http://www.ks.uiuc.edu/Development/MDTools/catdcd/
>>
>> Best,
>> Thanassis
>>
>>
>>> Hi all,
>>>
>>> I have a solvated system,need to run long simulations using NAMD and
>>> want to save only the protein coodinates in my DCD file.
>>> I searched about this but could not find anything related to saving
>>> DCD files without water moelcule coordinates.
>>> I will greatly appreciate, if someone help me with this.
>>>
>>> Thank you in advance
>>> Lisa
>>>
>>>
>>
>>
>>
>> Athanassios Stavrakoudis
>> University of Ioannina web: http://stavrakoudis.econ.uoi.gr/
>> Department of Economics e-mail: mailto:astavrak_at_cc.uoi.gr
>> GR-45110, Ioannina tel: +30 265 100 5935
>> GREECE fax: +30 265 100 5092
>>
>
>
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