[gmx-users] Energy Minimization

[Justin Lemkul]

On 11/3/16 10:11 AM, Mishelle Oña wrote:
> Positive values of potential energy and I am in vacuo.

Your outcome is exactly what you should expect.  Energies can be positive, and 
almost always are when doing work in vacuo.  The net negative energy in 
condensed phase is driven by attractive solute-solvent and solvent-solvent 
interactions, of which you have none in the gas phase.

-Justin

> Mishelle
>
>
>
> Sent from my Samsung device
>
>
> -------- Original message --------
> From: Justin Lemkul <jalemkul at vt.edu>
> Date: 11/03/2016 08:43 (GMT-05:00)
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Energy Minimization
>
>
>
> On 11/2/16 9:40 PM, Mishelle Oña wrote:
>> Hello
>>
>> I have a question about energy minimization tool. I am modelling a polymer and I use a force field I have developed. I have run a EM and got positive values. Can you help me with this?
>>
>
> Positive values for what?  Are you in vacuo or in solvent?
>
> -Justin
>
> --
> ==================================================
>
> 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
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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 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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