VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 01 2012 - 12:33:19 CDT

Hi,
  Regarding b), NAMD doesn't "recognize" anything. You will have
to have a PSF and matching parameter files so that NAMD can compute
the right energies. NAMD can't guess anything, it only reads what
you give it. If you have prepared a correct PSF and associated
parameter files, etc, then you should get correct results from NAMD.

Cheers,
  John Stone
  vmd_at_k.uiuc.edu

On Mon, Oct 01, 2012 at 06:39:43PM +0200, lloyd riggs wrote:
>
> Dear anyone whom might help,
>
> I had mentioned in a couple e-mails what I am doing now.
>
> My questions, as I found a main problem.
>
> a) is there a way to suppress the guessing atoms portion of the autopsf in VMD . I have somewhat of a coarse grained system, (some Carbon-polar H are merged into a gromacs trajectory as a composite atom)
>
> b) If I do succeed in getting this, with the gromacs traj loaded through the NAMDenergy plug in VMD, does it recognize coarse grained info, the info just from the trajectory generated, or will it act as if the C's are missing hydrogens (ie the energy calculations would be erroneous)?
>
> Basically it just guesses the missing atoms, when I do not need them in combo with the trajectory, but then I do not know how to suppress this, even as a command line, and have dug through the literature provided, as well as the mail list archives.
>
> Sincerely,
>
> Stephan Watkins 

-- 
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