Re: how to save a DCD file without water in NAMD ?

From: Lisa Brown (lisa.brown2009_at_gmail.com)
Date: Fri Aug 13 2010 - 11:02:36 CDT

Thank you all. Axel and Athanassios :thanks a lot for encouraging me.

2010/8/13 Athanassios Stavrakoudis <astavrak_at_cc.uoi.gr>:
> Hi Lisa,
>
> As Alex has already pointed out, if you needed it, there always a way...
> OK, the solution I propose takes me back to early 90's (I smile...),
> with those Silicon Graphics workstations supplied with the (then)
> "huge" disk of 1 Gbyte...
>
>
>
> 1. Typically, an MD trajectory will lead to some thousands of frames,
>   mayby 1000, or even 100000 if not more.
>   Estimate how many solvated frames can you afford. Let's say 100.
>
> 2. Run a simulation and store 100 solvated frames.
>
> 3. Keep only the solute from the .dcd file and discard the solvent.
>
> 4. Use the restart files to restart your simulation for another 100 frames
>
> 5. Repeat the cycle as many times as necessary, collecting this small .dcd
> files.
>
> 6. At the end, combine the .dcd files.
>
> This can be real time consuming, but in case of "low disk" emergency,
> it might help.
>
> I have to confess that with all of these papers around analyzing
> the importance of water in biological structure/function,
> the all cause I see for such a procedure is the "low disk" nightmare!
>
> On the other hand, you might consider implicit solvation strategies.
> In the past, I have used TINKER for this purpose.
> http://dasher.wustl.edu/tinker/
>
> Good luck,
> Thanassis
>
>
>
>> 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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