VMD-L Mailing List

From: lloyd riggs (lloyd.riggs_at_gmx.ch)
Date: Mon Oct 01 2012 - 12:10:05 CDT

Sorry Im an idiot with some things sometimes. I went back and the command line has the answer to a) But I still dont know the b) answer however the gromacs and dock software I mixed, the gromacs makes composite non-polar hydrogens.

Stephan

-------- Original-Nachricht --------
Datum: Mon, 01 Oct 2012 18:39:43 +0200
Von: "lloyd riggs" <lloyd.riggs_at_gmx.ch>
An: vmd-l_at_ks.uiuc.edu
Betreff: RE:psfgen and CG

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