Another thing you cann try is equilibrating the system with a classical MD run at first ... It should work.
On Mon, Dec 7, 2009 at 5:10 PM, Szyja, B.M. <[email protected]> wrote: > Hi Sufian, > > In general, if the random distribution of molecules gives us the system > close enough to it's optimal geometry (not necessarily in its minimum), you > could start MD without prior optimization, and you only need the > equilibration run to "take care" of the proper geometry. But if you observe > such jumps in temperature, it usually means too much or too close contacts. > I would suggest you to do at least a couple of optimization steps and then > try again. From my experience I can say that water is quite tricky solvent, > it is not only due to the density of the simulated cell, but also the > relative orientation of molecules (presence of hydrogen bonds network) can > play an important role. > > Success! > Bartek > > ________________________________________ > From: [email protected] [[email protected]] > Sent: Monday, December 07, 2009 11:32 AM > To: [email protected] > Cc: [email protected] > Subject: RE: [SIESTA-L] Energy flauctuation in MD > > Hi Bartek > i am planning to optimize the net structure (16H2O + Formaamide) after i > "shake" the unit cell with those water molecules only > random distribution of water molecules were chosen alone firstly, > I really do not know if i need to optimize H2O molecules before MD run? > > yours, > sufian > > > > Hi Sufian, > > > > My guess is the geometry being too far from optimal. Have you optimized > > the system (atomic coordinates and/or cell size) before the MD run? > > > > Cheers, > > Bartek > > > > ________________________________________ > > From: [email protected] [[email protected]] > > Sent: Monday, December 07, 2009 10:58 AM > > To: [email protected] > > Cc: [email protected] > > Subject: Re: [SIESTA-L] Energy flauctuation in MD > > > > Hi Andrey > > > > I have 16-H2O molecule in my unit cell, i am trying to cool the system > > down from 1000K to 300K to be more realistic. The problem still there, > > the > > temperature goes very high and won't stop at the target temperature, i > > tried to use annealing, Nose,... all those options give the same > problem, > > i am wondering if there is any unseen option that can be used to fix > this > > problem? > > > > yours, > > sufain > >> > >> > >>> Hi Sufian, > >>> > >>> How many molecules does your "bunch" contain? It's normal to have > >>> temperature fluctuations of ~T/sqrt(N), where N is the number of > >>> particles. Also I encountered non-physical temperature fluctuations > >>> when initial temperature of run was not equal to final temperature. > >>> Seems that Nose thermostat in Siesta is not capable to implement > >>> temperature gradients. And the final remark - if you want to model > >>> gas-liquid phase transition, Siesta might not be the right tool to do > >>> it, since it needs a big supercell and large simulation time. > >>> > >>> Cheers, > >>> Andrey. > >>> > >>>> Dear Siesta Users > >>>> > >>>> I am trying to run a molecular dynamics simulation for a bunch of H2O > >>>> molecules,i chose the Tini =800 K and Tfin= 300 K my run starts > >>>> normally for the first one or two steps. but after that a huge > >>>> fluctuations in temperature appear, it reached a couple of thousands > >>>> of kelvins i,tried many options but i still has the same problem, > >>>> can any body assist me in this problem? > >>>> Thank you all, > >>>> > >>>> sufian > >>>> > >>> > >> > >> > > > > > > > > >
