From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Mon Aug 13 2007 - 04:55:35 CDT
Sorry I meant that ICNTRL(9)....NATOM-NFREAT was zero in the dcd file. So
NFREAT = NATOM
On 8/13/07, Joshua D. Moore <jdmoore_at_unity.ncsu.edu> wrote:
>
> Hi,
>
> When I run simulations with fixed atoms, they appear to be written in the
> dcd file the same as if they were not fixed. The sizes of the dcd files are
> the same also as the nonfixed.
>
> The atoms are definitely fixed however
>
> When I do a grep for 'FIXED' on the output I see this, and the energies
> are definitely not being calculated I expect.
>
> Info: FIXED ATOMS ACTIVE
> Info: 2800 FIXED ATOMS
> Info: 2800 HYDROGEN GROUPS WITH ALL ATOMS FIXED
>
> The NFREAT variable (ICNTRL(9)) also is zero in the DCD file.
>
> I also know they are fixed because I can see that they are. Is there
> something special that you need to do to turn the feature on for the dcd
> file to only write the coordiates of the moving atoms?
>
> I am fixing them by doing
>
> fixedAtoms on
> fixedAtomsCol O
>
> and then changing the occupancy column in the pdb file to be '0.00' for
> the atoms I want to let move.
>
> Thanks.
>
> Josh
>
>
>
> --
> ------------------------------------------------
> Joshua D. Moore
> Graduate Student
> North Carolina State University
> Dept. of Chemical and Biomolecular Engineering
> Box 7905 Centennial Campus
> Engineering Building I
> 911 Partners Way
> Raleigh, NC 27695-7905
> Phone: (919) 513-2051
> Fax: (919) 513-2470
> Email: jdmoore_at_unity.ncsu.edu
> ------------------------------------------------
>
-- ------------------------------------------------ Joshua D. Moore Graduate Student North Carolina State University Dept. of Chemical and Biomolecular Engineering Box 7905 Centennial Campus Engineering Building I 911 Partners Way Raleigh, NC 27695-7905 Phone: (919) 513-2051 Fax: (919) 513-2470 Email: jdmoore_at_unity.ncsu.edu ------------------------------------------------
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