From: Lisa Brown (lisa.brown2009_at_gmail.com)
Date: Fri Aug 13 2010 - 08:06:36 CDT
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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