From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Feb 26 2013 - 20:58:04 CST
What are the values in UAsim-ernest-step2.restart.xsc?
If step2 didn't crash, you need to figure out what changed in your step3
configuration.
From: Patricia Campbell [mailto:patricia.campbellsoup_at_gmail.com]
Sent: Tuesday, February 26, 2013 8:55 PM
To: JC Gumbart
Subject: Re: namd-l: DCD file doubles a monomer
Hello JC
Thanks for your reply. A previous response also mentioned this but he said
that it seemed fine when I showed my values. Maybe you can give a different
perspective. Thanks. Here are my values:
cellBasisVector1 249.67699432373047 0 0
cellBasisVector2 0 228.1929931640625 0
cellBasisVector3 0 0 299.4889907836914
cellOrigin -157.62777709960938 -186.60768127441406 -69.33441925048828
And some values from my PDB file:
CRYST1 249.365 227.773 298.847 90.00 90.00 90.00 P 1 1
ATOM 1 N VAL P 122 -163.391-161.947 -66.564 1.00 0.00 P1
N
Minmax are:
{-282.72198486328125 -300.885009765625 -217.57899475097656}
{-33.362998962402344 -73.1259994506836 81.26300048828125}
Here is my namd file:
### Docking -- Step 3
set PSFFILE ionized.psf
set PDBFILE step2_all.pdb
set GRIDPDB step2-grid.pdb
set DIEL 1
set SCALING_1_4 1.0
set ITEMP 0
set FTEMP 300
set GRIDFILE nonNAMDbigger-grid.dx
set GSCALE 0.3
set EXTRAB {step2-extrabonds.txt step2-cispeptide.txt step2-chirality.txt}
set CONSPDB step2solvent.pdb
set CONSCOL B
set FIXPDB 0
set INPUTNAME UAsim-ernest-step2
set OUTPUTNAME UAsim-ernest-step3
set TS 500000
set MS 2000
set MARGIN 0
####################################
structure $PSFFILE
coordinates $PDBFILE
paraTypeCharmm on
parameters par_all27_prot_lipid_na.inp
if {[info exists INPUTNAME]} {
BinVelocities $INPUTNAME.restart.vel
BinCoordinates $INPUTNAME.restart.coor
ExtendedSystem $INPUTNAME.restart.xsc
} else {
temperature $ITEMP
cellBasisVector1 249.67699432373047 0 0
cellBasisVector2 0 228.1929931640625 0
cellBasisVector3 0 0 299.4889907836914
cellOrigin -157.62777709960938 -186.60768127441406 -69.33441925048828
}
PME yes
PMEGridSpacing 1.0
PMEPencils 1
wrapAll on
source mdff_template.namd
On Tue, Feb 26, 2013 at 8:49 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
I bet your cellBasisVectors are wrong. Check the dimensions of your system.
On Feb 26, 2013, at 1:09 PM, Patricia Campbell wrote:
Hello,
I am trying to run a large simulation comprised of over 20 monomers (1.6
million atoms total after solvation/ionization). The simulation never makes
it past the first step of equilibration before crashing due to atom
velocity. Recently, I tried running the structure through 20000 minimization
steps. I checked the structure and I noticed that the dcd file adds a
monomer on top of another monomer after the first frame. When the
equilibration crashes its due to atoms located in either of these two
monomers. The two monomers are right on top of one another. I have no idea
how this is happening. I also tried running a minimization in vacuo and the
same thing happened after the first frame. Furthermore, I tried deleting the
second monomer out of the PDB file but then was unable to load the PDB file
into the PSF file in VMD. Is there any way to stop this??? Thank you.
-- Patricia Campbell 706-577-3754 patricia.campbellsoup_at_gmail.com -- Patricia Campbell 706-577-3754 patricia.campbellsoup_at_gmail.com
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