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 >>>> >>> >> >> > > >
