[gmx-users] genion command
jalemkul at vt.edu
Tue May 16 16:08:26 CEST 2017
On 5/16/17 12:55 AM, Saumyak Mukherjee wrote:
> Hello Diana,
> You may try using the -conc flag in genion program to specify your salt
> concentration, along with -nname and -pname flags.
The -nname and -pname options are irrelevant here.
If there are fewer than 1000 waters in the system, I doubt the number of ions
has been calculated correctly, though. Compare with -conc 0.6 to see if the
math is right, and make sure that the solvent is actually being replaced, not
> Best wishes,
> On 16 May 2017 at 10:18, diana p <diana64mp at gmail.com> wrote:
>> Dear gmx users,
>> I want to simulate 0.6M CaCL2 aqueous solution. To add the ions I use
>> genion command and add 720 CL and 360 Ca ions respectively to the system of
>> pure 12568 water molecules.But on running the command genion I get error
>> Program genion, VERSION 4.6.5
>> Source code file: /build/buildd/gromacs-4.6.5/src/tools/gmx_genion.c,
>> Fatal error:
>> No more replaceable solvent!
>> How should I add ions in the system.I would be more than pleased if someone
>> could guid me.
>> Thank You in advance
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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