[gmx-users] Error running GMX 5.14

[Justin Lemkul]

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
> 
> [ 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: "Justin Lemkul" <jalemkul at vt.edu>
> To: "gmx-users" <gmx-users at 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." <smithmd at ornl.gov>
>> To: "gmx-users" <gmx-users at 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-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sergio Manzetti <sergio.manzetti at fjordforsk.no>
>> Sent: Tuesday, June 20, 2017 7:48 AM
>> To: gmx-users at 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================