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

From: Athanassios Stavrakoudis (astavrak_at_cc.uoi.gr)
Date: Fri Aug 13 2010 - 10:23:01 CDT

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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