<html><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><META name="Author" content="Novell GroupWise WebAccess"></head><body style='font-family: Helvetica, Arial, sans-serif; font-size: 13px; '>Hello,<br>I've been following the discussion for a while and came just to think about another problem:<br>What about the PME - isn't that messing up the energy conservation?<br>I believe that that's also a non-conservative force -or am I completely wrong?<br>Cheers,<br>Peter<br><br><br><br/><div style='clear: both;'><HTML><HEAD>
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<DIV>Dr Peter Ahlström</DIV>
<DIV>University of Borås</DIV>
<DIV>SE-501 90 Borås</DIV>
<DIV>Sweden</DIV>
<DIV>+46 33 435 4675</DIV></BODY></HTML></div><br/>>>> David van der Spoel <spoel@xray.bmc.uu.se> 06/07/15 5:58 PM >>><br>On 02/06/15 13:45, Shirts, Michael R. (mrs5pt) wrote:<br>>> How do we run more NVE than with the settings below?<br>><br>> tcoupl = Nose-Hoover<br>><br>><br>> Would make it not NVE.<br>><br>> Do you mean the conserved quantity isn't conserved? Energy certainly<br>> won't be conserved with Nose-Hoover.<br>Disturbing altogether.<br><br>Is there any reason that md-vv would be better than the md integrator <br>for energy conservation?<br><br>><br>> Best,<br>> ~~~~~~~~~~~~<br>> Michael Shirts<br>> Associate Professor<br>> Department of Chemical Engineering<br>> University of Virginia<br>> michael.shirts@virginia.edu<br>> (434) 243-1821<br>><br>><br>><br>> On 6/2/15, 7:22 AM, "David van der Spoel" <spoel@xray.bmc.uu.se> wrote:<br>><br>>> On 02/06/15 12:47, Berk Hess wrote:<br>>>> Hi,<br>>>><br>>>> So this is not using SETTLE or LINCS?<br>>>> With SETTLE this is a known issue.<br>>> No this is flexible organic molecules at contant volume.<br>>><br>>>><br>>>> Did you try running NVE?<br>>> How do we run more NVE than with the settings below?<br>>><br>>><br>>>><br>>>> Cheers,<br>>>><br>>>> Berk<br>>>><br>>>> On 2015-06-02 12:43, David van der Spoel wrote:<br>>>>> Hi,<br>>>>><br>>>>> this is in between a user and a developer query. We find that for<br>>>>> flexible liquid simulations using gromacs 5.0.4/single precision the<br>>>>> energy conservation gets WORSE with decreasing time step. A plot<br>>>>> showing this is in<br>>>>> http://folding.bmc.uu.se/images/Econserved-timestep.xvg or<br>>>>> http://folding.bmc.uu.se/images/Econserved-timestep.pdf<br>>>>><br>>>>> MDP settings<br>>>>> coulombtype = PME<br>>>>> coulomb-modifier = Potential-shift<br>>>>> rcoulomb-switch = 0<br>>>>> rcoulomb = 1.1<br>>>>> epsilon-r = 1<br>>>>> epsilon-rf = inf<br>>>>> vdw-type = PME<br>>>>> vdw-modifier = Potential-shift<br>>>>> rvdw-switch = 0<br>>>>> rvdw = 1.1<br>>>>> tcoupl = Nose-Hoover<br>>>>> nsttcouple = 10<br>>>>> nh-chain-length = 1<br>>>>> pcoupl = No<br>>>>> ref-t: 298.15<br>>>>> tau-t: 0.5<br>>>>><br>>>>> Any clues whether we are doing something wrong? Or is there a bug?<br>>>>><br>>>>> Cheers,<br>>>><br>>><br>>><br>>> --<br>>> David van der Spoel, Ph.D., Professor of Biology<br>>> Dept. of Cell & Molec. Biol., Uppsala University.<br>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>>> spoel@xray.bmc.uu.se http://folding.bmc.uu.se<br>>> --<br>>> Gromacs Developers mailing list<br>>><br>>> * Please search the archive at<br>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before<br>>> posting!<br>>><br>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>>><br>>> * For (un)subscribe requests visit<br>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers<br>>> or send a mail to gmx-developers-request@gromacs.org.<br>><br><br><br>-- <br>David van der Spoel, Ph.D., Professor of Biology<br>Dept. of Cell & Molec. Biol., Uppsala University.<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>spoel@xray.bmc.uu.se http://folding.bmc.uu.se<br>-- <br>Gromacs Developers mailing list<br><br>* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before posting!<br><br>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br><br>* For (un)subscribe requests visit<br>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers or send a mail to gmx-developers-request@gromacs.org.<br><br></body></html>