[gmx-users] Re: Have your ever got a real NVE simulation (good energy conservation) in gromacs?
S. Alireza Bagherzadeh
s.a.bagherzadeh.h at gmail.com
Fri May 24 09:24:15 CEST 2013
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:
*S. Alireza Bagherzadeh, M.A.Sc. <https://circle.ubc.ca/handle/2429/26269>
*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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> 1. Re:The effect of coulomb-modifier and vdw-modifier in Verlet
> cutoff scheme (Bin Liu)
> 2. Re: file not found (Humayun Arafat)
> Have your ever got a real NVE simulation (good energy
> conservation) in gromacs? (cyberjhon)
> 4. On using CO2 as solvent (Bao Kai)
> 5. Re: On using CO2 as solvent (Justin Lemkul)
> 6. tpr of extend simulation (maggin)
> 7. Re: Have your ever got a real NVE simulation (good energy
> conservation) in gromacs? (Mark Abraham)
> 8. g_hbond (maggin)
> 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
> 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
> John Michael Espinsoa Duran
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> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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