On 9/12/12 2:38 PM, Bharath K. Srikanth wrote:
Hi
I am trying to run a simulation of the self-assembly of a course-grained
lipid bilayer using GROMACS. So far, I have made a box of DSPC lipid
molecules (7.5 x 7.5 x 7.5, 128 molecules). I have also added water
molecules using the genbox command (768 water molecules added), and named
the coordinate file as waterbox.gro.
For the next step, when I try to run a minimization, I get an error as
follows:
Fatal error:
number of coordinates in coordinate file (waterbox.gro, 2560)
does not match topology (dspc.top, 1792)
What I understood from this was that the water molecules (768 water
molecules = 2560-1792) added by genbox had not been updated to the
topology file. However, my topology file reads as follows:
#include "martini_v2.1.itp"
#include "martini_v2.0_lipids.itp"
[ system ]
DSPC BILAYER SELF-ASSEMBLY
[ molecules ]
DSPC 128
; W 768
which indicates that 768 water molecules have, indeed, been added to the
topology file- this appears to be fine. Is there anything I'm missing out
on here?
The "W" line is commented out, so grompp doesn't read the fact that there are
768 W particles at all.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
