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