From: Pavan G (pavan.namd_at_gmail.com)
Date: Fri Jun 25 2010 - 09:19:42 CDT
Hello Peter,
I tried regenerating angles and dihedrals with the Charmm script using the
'generate protein setup' command but it didn't add the terminal OT1--C--OT2
angle and relevant dihedrals. So I manually added them in to the PSF file.
This fixed the problem in the sense that I managed to heat the system (npt)
to 400K w/o crashing. But now when I look at the output file, the pressure
lines are all 0's.
PRESSURE: 1000 0 0 0 0 0 0 0 0 0
PRESSURE: 2000 0 0 0 0 0 0 0 0 0
PRESSURE: 3000 0 0 0 0 0 0 0 0 0
PRESSURE: 4000 0 0 0 0 0 0 0 0 0
..........
PRESSURE: 77000 0 0 0 0 0 0 0 0 0
PRESSURE: 78000 0 0 0 0 0 0 0 0 0
PRESSURE: 79000 0 0 0 0 0 0 0 0 0
PRESSURE: 80000 0 0 0 0 0 0 0 0 0
PRESSURE: 81000 0 0 0 0 0 0 0 0 0
Could the manual addition of angles and dihedrals be the reason behind this
behavior? The trajectory looks fine though. The RMSD increases as the
temperature is increased. In fact if I don't look at the output file
everything looks fine :)
Any comments are greatly appreciated.
Pavan
On Wed, Jun 16, 2010 at 12:48 PM, Peter Freddolino <petefred_at_ks.uiuc.edu>wrote:
> Hi Pavan,
> this usually happens if you use a CMAP topology file but do not
> regenerate angles and dihedrals after psf generation. It would help if
> you could post the name of the topology file that you're using, and the
> version of vmd.
> Best,
> Peter
>
> On 06/16/2010 11:32 AM, Pavan G wrote:
> > Hello All,
> > I am trying to run a NAMD simulation of a protein in water with
> > Charmm27 ff. The terminal carboxyl carbon and two oxygens look fine in
> > the starting structure but as soon as the minimization starts the two
> > oxygens come close to each other and the simulation fails later when I
> > start NVT and/or heat beyond 250K. The charges on the oxygens are
> > -0.67 each and charge on carboxyl carbon is 0.34 as expected. I fail
> > to see why minimization would force two highly (both negative) charged
> > atoms close to each other. Any help would be appreciated. The C
> > terminal residue was created with the cter patch in Charmm.
> > Thanks,
> > Pavan
> >
>
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