[gmx-users] NVT problem

[Andres Ortega Guerrero]

Hi Justin, 

I have done a 1ns MD with DOX + water + CL ion , the topology didn´t present any problem, 

i also did what you suggested, a -DFLEXIBLE EM and settle EM, but when i was trying to do my nvt.mdp

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.003859, max 0.176655 (between atoms 47397 and 47398)
bonds that rotated more than 30 degrees:

WARNING: Listed nonbonded interaction between particles 7156 and 7175
at distance 3f which is larger than the table limit 3f nm.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

this are the warning that appear, so based on this, the main problem seems like to be my structure  right?
maybe, the DOX is misplaced or something like that, so should i prepare again the .gro files?

Thanks in advance Justin, 

Andres Ortega
Universidad del Valle  (Colombia)
Bionanoelectronics Research Group

> Date: Sat, 15 Mar 2014 16:02:43 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] NVT problem
> 
> 
> 
> On 3/15/14, 3:59 PM, Andres Ortega Guerrero wrote:
> > Thank you Justin
> >
> > 1) Yes it can get a lower emtol
> >
> > 4)i´m using OPLS-AA ,FF
> > 5) DOX is Doxorubicin,
> >
> > DOX.itp :
> >
> > 1) The structure was optimize with Gaussian and the charges was calculated to 1,
> > 2) DOX.itp was generated by MKTOP, but i have to select 2 different atoms, and find the Diheradrals that was missing
> >
> 
> A simple simulation of DOX in water will indicate whether the topology is stable.
> 
> The larger issue is using flexible water for EM and not minimizing again with 
> constraints.  Inspect the energy-minimized geometry; I suspect you will find 
> some distorted waters.  Given that NVT fails immediately, it suggests that there 
> is an unresolvable geometry problem, despite the apparent success of EM.
> 
> -Justin
> 
> >
> > Thanks Justin
> >
> >> Date: Sat, 15 Mar 2014 15:41:11 -0400
> >> From: jalemkul at vt.edu
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] NVT problem
> >>
> >>
> >>
> >> On 3/15/14, 3:37 PM, Andres Ortega Guerrero wrote:
> >>> Thank you Justin for Your Help, and advice, i have already the modification on the nvt.mdp that you suggest,  but the problem is still there, my system has about 150.000 atoms , and for the energy minization i used DFLEXIBLE, and  emtol was ajusted to 1000, i take a look to the steep0.pdb that gromacs produce, and there are atoms out of the box, but the DOX molecule is OK
> >>>
> >>> what would you suggest?
> >>> - a emtol lower?
> >>> - a water and dox md? ( maybe the DOX.itp can be the problem) ?
> >>>
> >>
> >> Several ideas/questions:
> >>
> >> 1. Does energy minimization complete adequately?  Can it proceed further (lower
> >> emtol than 1000)?
> >> 2. If you have used flexible water, you should re-minimize with
> >> constraints/rigid water.  It is common that a minimized system has badly
> >> distorted the geometry of one or more water molecules.
> >> 3. "Out of the box" is not an issue if you are using PBC, because no such thing
> >> exists.  If something has gone flying out of the rendered unit cell (i.e. large
> >> coordinates), that suggests severe instability of the initial configuration and
> >> would be a likely source of the problem.
> >> 4. What force field are you using?
> >> 5. What is the source of your DOX.itp parameters?  What is DOX?
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA 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
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
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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 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
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