[gmx-users] Getting started / tutorial speptide example g_energy and xmgrace

DaJustice1 at aol.com DaJustice1 at aol.com
Tue May 13 15:03:01 CEST 2003

Hello all,

I am simulating Ru(NH3)5 modified Cyt c (HIS 33) which grompp says has a 
charge of 9.0.   I minimized the system using steep and cg with PME, without 
using counter ions.   I then ran a simulation of sed system, and it worked 
fine (as far as I can tell).  I don't think it should have though...   From 
what I have read in archives about PME, it needs to have a neutralized system 
to work correctly.   I figured the simulation ran just as a fluke, so I 
neutralized the system with genion and updated the topology and gro.   After 
the updates I ran grompp which gave no warning of a nonzero charged system, 
but when I tried to run energy minimization (cg) the message was: "Fatal 
error: ci = -2147483648 should be in 0 .. 391 [FILE nsgrid.c, LINE 210]".   
Steep also erred out.   The only time the message would go away is when I 
used cut-off.   Is it the compile of fftw, the Cl ions I added, or something 
else?   The mdp file is as follows:

title                =   ${MOL}
cpp                  =   /usr/bin/cpp
define               =   -DFLEX_SPC
constraints          =   none
integrator           =   cg
dt                   =   0.002     ; ps!
nsteps               =   1000
nstlist              =   10
ns_type              =   grid
nstcgsteep               =   500
rlist                =   .9
rcoulomb             =   .9
rvdw                 =   .9
pbc                  = xyz
coulombtype          = PME
;        Energy minimizing stuff
emtol                =   100.0
emstep               =   0.01

Thank you,
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