RE: problems-periodic cell

From: Irene Newhouse (einew_at_hotmail.com)
Date: Tue Jan 01 2008 - 14:41:36 CST

If you are running NPT, check the most recent .xsc file for the current unit cell parameters. You may have to adjust the PME grid values.
 
Irene Newhouse> CC: namd-l_at_ks.uiuc.edu> From: gillescche_at_gmail.com> To: corrjose_at_gmail.com> Subject: Re: namd-l: problems-periodic cell> Date: Tue, 1 Jan 2008 13:23:25 -0500> > Jose,> > You can potentially get by this by adding> > margin 1.0> > to you *.conf file. I continue to increase this number until I no > longer receive this message.> > Best> > Chris> > On Jan 1, 2008, at 10:30 AM, jose correa wrote:> > > Dear all> > I am running a NAMD simulacion, but the program yield this message:> >> > OPENING EXTENDED SYSTEM TRAJECTORY FILE> > FATAL ERROR: Periodic cell has become too small for original patch > > grid!> > Possible solutions are to restart from a recent checkpoint,> > increase margin, or disable useFlexibleCell for liquid simulation.> > Stack Traceback:> > [0] _ZN9HomePatch14positionsReadyEi+0x6e [0x824ee3a]> > [1] _ZN9Sequencer17runComputeObjectsEii+0xcc [0x82bbd5c]> > [2] _ZN9Sequencer9integrateEv+0xb04 [0x82c0894]> > [3] _ZN9Sequencer9algorithmEv+0x334 [0x82bb660]> > [4] _ZN9Sequencer9threadRunEPS_+0xc [0x82ccd1c]> > [5] namd2 [0x831aa19]> > [6] Charm++ Runtime: Converse thread (qt_args+0x72 [0x83939ca])> > ~> > Can somebody help me?, please.> > Best wishes> > Jose Correa-Basurto> >> >>
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