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, <[email protected]> wrote: > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re:The effect of coulomb-modifier and vdw-modifier in Verlet > cutoff scheme (Bin Liu) > 2. Re: file not found (Humayun Arafat) > 3. > 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 <[email protected]> > Subject: [gmx-users] Have your ever got a real NVE simulation (good > energy conservation) in gromacs? > To: [email protected] > Message-ID: <[email protected]> > 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 > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Have-your-ever-got-a-real-NVE-simulation-good-energy-conservation-in-gromacs-tp5008501.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > > ------------------------------ > > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
