[gmx-users] Re: Have your ever got a real NVE simulation (good energy conservation) in gromacs?

[S. Alireza Bagherzadeh]

Hi John,

I was dealing with this issue recently. Have you considered these points?

   1. Run gromacs in double-precision (mdrun_d)
   2. use PME-Switch for the treatment of the Coulombic interaction
   3. follow the guidelines from here:
   http://www.gromacs.org/Documentation/Terminology/NVE




Regards,
-- 
*S. Alireza Bagherzadeh, M.A.Sc. <https://circle.ubc.ca/handle/2429/26269>
*
**
*PhD Candidate
*
**
*Dept. of Chem. & Bio. Eng. <http://www.chbe.ubc.ca/>*
**
*University of BC <http://www.ubc.ca/>
*





On Thu, May 23, 2013 at 11:34 PM, <gmx-users-request at gromacs.org> wrote:

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> ----------------------------------------------------------------------
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> Message: 3
> Date: Thu, 23 May 2013 14:59:11 -0700 (PDT)
> From: cyberjhon <cyberjhon at hotmail.com>
> Subject: [gmx-users] Have your ever got a real NVE simulation (good
>         energy conservation) in gromacs?
> To: gmx-users at gromacs.org
> Message-ID: <1369346351811-5008501.post at n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Guys
>
> I have been trying by all means to get a real good Energy conservation in
> NVE simulations using gromacs
> but it has been almost impossible for me.
> I have tried many different combinations of Coulomb and VdW parameters and
> changed the cut off radius and nothing.
> 1. Have you ever obtained energy conservation in Gromacs?
> 2. Under what conditions ? for what system?
> 2. Do you have a set of parameters that works to obtain energy
> conservation?
> if you can share with me the mdp file, I will appreciate it.
> My system is Human Papiloma Virus  virus-like particle T=1 inmersed in SPC
> water.
>
> Thanks
>
> John Michael Espinsoa Duran
>
>
>
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