On 6/20/17 8:27 AM, Sergio Manzetti wrote:
I can add ions to the final system, after having simulated it without ions. But
what would the point be?
This is the strange thing, genion treats only tpr files, and not gro files with
solvated states
The .tpr file fed to genion is that of a solvated .gro file, and a .tpr file is
necessary so that genion knows the connectivity of each molecule. That's how it
removes whole molecules at a time. If you haven't used genion properly (or at
all), then you can expect a problematic result. See basic tutorials if this
workflow is unclear.
-Justin
Sergio Manzetti
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[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ]
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From: "Justin Lemkul" <jalem...@vt.edu>
To: "gmx-users" <gmx-us...@gromacs.org>
Sent: Tuesday, June 20, 2017 2:29:36 PM
Subject: Re: [gmx-users] Error running GMX 5.14
On 6/20/17 8:22 AM, Sergio Manzetti wrote:
Maybe someone can suggest a method to add ions to the system without that they
appear as water molecules?
The job of genion is to replace water molecules with ions. There is no way that
grompp can turn one into the other; you would get a fatal error about
mismatching names and/or numbers of atoms in the case of a flawed topology. I
suggest you verify the contents of your topology (which should have been
automatically updated by genion to be correct) and any output from grompp to
make sure you're not ignoring any additional problems. Then check that your
interpretation of atom numbers is correct. I find it extremely unlikely that
mdrun is complaining about trying to SETTLE an ion (it's topologically
impossible).
-Justin
The em looks like this:
define =
integrator = steep
emtol = 100.0
emstep = 0.0001
nsteps = 10000
; output frequency
nstxout = 50
nstvout = 0
nstfout = 0
nstlog = 50
nstenergy = 50
nstxtcout = 0
xtc_grps = system
;
nstlist = 10
pbc = xyz
rlist = 1.4
cutoff-scheme = group
coulombtype = PME
rcoulomb = 1.4
vdwtype = cut-off
rvdw = 1.4
DispCorr = EnerPres
;
constraints = none
constraint_algorithm = LINCS
implicit_solvent = no
E_x =
E_y =
E_z =
Sergio Manzetti
[ http://www.fjordforsk.no/logo_hr2.jpg ]
[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory
] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ]
From: "Smith, Micholas D." <smit...@ornl.gov>
To: "gmx-users" <gmx-us...@gromacs.org>
Sent: Tuesday, June 20, 2017 2:09:08 PM
Subject: Re: [gmx-users] Error running GMX 5.14
What does your *.mdp file look like? Its hard to judge what the next step
should be from what you've given so far.
-Micholas
===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
________________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sergio Manzetti
<sergio.manze...@fjordforsk.no>
Sent: Tuesday, June 20, 2017 7:48 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Error running GMX 5.14
Hi, I have a system with DNA and water, and given the charge of the DNA of -20,
genion was used to add +20 charge to the gro file. The energy minimization step
gives then a warning:
WARNING 2 [file em.mdp]:
The sum of the two largest charge group radii (16.704304) is larger than
rlist (1.200000)
Which is the ignored using maxwarn option.
When getting to the em step:
Fatal error:
step 25: Water molecule starting at atom 31535 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
What is the best approach here to correct this?
Thanks!
Sergio Manzetti
[ http://www.fjordforsk.no/logo_hr2.jpg ]
[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory
] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ]
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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