[gmx-users] potential energy doesn't have negative value

[Afsane Farhadi]

thank you so much Mr.justin 

Sent from Yahoo Mail on Android 
 
  On Sun, Mar 15, 2020 at 3:38, Justin Lemkul<jalemkul at vt.edu> wrote:   

On 3/14/20 8:05 PM, Afsane Farhadi wrote:
> what do I have to do for solving this mater? I want to use a opls as forcefield.  how can I find that forcefield for methyldiethanolamine?

http://zarbi.chem.yale.edu/ligpargen/

-Justin

> Sent from Yahoo Mail on Android
>  
>    On Sun, Mar 15, 2020 at 3:29, Justin Lemkul<jalemkul at vt.edu> wrote:
>
> On 3/14/20 7:15 PM, Afsane Farhadi wrote:
>> I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the potential energy is positive.  the mdp file is attached.
> The mailing list does not accept attachments.
>
> ATB does produce GROMOS-compatible force fields, but it is always up to
> the user to determine if the parameters are suitable. A positive
> potential energy means that the intermolecular interactions are weak
> compared to the intramolecular (bonded) interactions. You can use gmx
> energy or look in the .log file to see the various contributions to the
> total potential energy.
>
> -Justin
>

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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