For thistasks there is also a freewere one named Packmol ... On Mon, Dec 7, 2009 at 8:14 PM, Ben Martin <[email protected]> wrote:
> I have found that if your initial configuration is distributed well enough, > then a classical MD thermalization isn't necessary....but you'll need a good > program that does that for you. If you already have a classical MD code > you're familiar with, then use that. Otherwise, the skew start method of > MOLDY (http://www.ccp5.ac.uk/librar.shtml#MOLDY) works really well. MOLDY > also has MD capability, but like I said the skew start method for generating > an initial configuration has been sufficient for me in SIESTA (although I > haven't used it for water). > > > On Mon, Dec 7, 2009 at 8:27 AM, N H <[email protected]> wrote: > >> 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 >>> >>>> >>> >>> >>> >> >>> >> >>> > >>> > >>> > >>> >>> >>> >> >
