<HTML><FONT FACE=arial,helvetica><FONT SIZE=2 FAMILY="SANSSERIF" FACE="Arial" LANG="0">I sent this under an erroneous tittle last time...<BR>
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Hello all,<BR>
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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:<BR>
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title = ${MOL}<BR>
cpp = /usr/bin/cpp<BR>
define = -DFLEX_SPC<BR>
constraints = none<BR>
integrator = cg<BR>
dt = 0.002 ; ps!<BR>
nsteps = 1000<BR>
nstlist = 10<BR>
ns_type = grid<BR>
nstcgsteep = 500<BR>
rlist = .9<BR>
rcoulomb = .9<BR>
rvdw = .9<BR>
pbc = xyz<BR>
coulombtype = PME<BR>
;<BR>
; Energy minimizing stuff<BR>
;<BR>
emtol = 100.0<BR>
emstep = 0.01<BR>
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Thank you,<BR>
David</FONT><FONT COLOR="#000000" style="BACKGROUND-COLOR: #ffffff" SIZE=3 FAMILY="SANSSERIF" FACE="Arial" LANG="0"><BR>
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