RE: DCD file doubles a monomer

From: JC Gumbart (
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


From: Patricia Campbell []
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


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 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 <> wrote:

I bet your cellBasisVectors are wrong. Check the dimensions of your system.


On Feb 26, 2013, at 1:09 PM, Patricia Campbell wrote:



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
Patricia Campbell

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:20:57 CST