[gmx-users] NVT problem

[Justin Lemkul]

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

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