On 1/15/14, 10:52 AM, Albert wrote:
Hello:
I found that the -norandom option in genion was no longer in 4.6.5:
genion -h
Option Filename Type Description
------------------------------------------------------------
-s topol.tpr Input Run input file: tpr tpb tpa
-n index.ndx Input, Opt. Index file
-o out.gro Output Structure file: gro g96 pdb etc.
-p topol.top In/Out, Opt. Topology file
Option Type Value Description
------------------------------------------------------
-[no]h bool yes Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-np int 0 Number of positive ions
-pname string NA Name of the positive ion
-pq int 1 Charge of the positive ion
-nn int 0 Number of negative ions
-nname string CL Name of the negative ion
-nq int -1 Charge of the negative ion
-rmin real 0.6 Minimum distance between ions
-seed int 1993 Seed for random number generator
-conc real 0 Specify salt concentration (mol/liter). This will
add sufficient ions to reach up to the specified
concentration as computed from the volume of the
cell in the input .tpr file. Overrides the -np
and -nn options.
-[no]neutral bool no This option will add enough ions to neutralize
the system. These ions are added on top of those
specified with -np/-nn or -conc.
I am just wondering does it means the pme methods would be automatically for ion
placement?
Non-random placement never really worked, so it was removed as an option. Now,
genion only places ions randomly.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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