[gmx-users] NVT problem

[Andres Ortega Guerrero]

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 


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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