[gmx-users] NVT problem
Andres Ortega Guerrero
og_andres15 at hotmail.com
Sat Mar 15 20:59:25 CET 2014
Thank you Justin
1) Yes it can get a lower emtol
4)i´m using OPLS-AA ,FF
5) DOX is Doxorubicin,
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
> 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 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
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users