Re: Re[2]: [gmx-users] RE: can gmx be used to simulation NaCl

2008-06-29 Thread Tsjerk Wassenaar
As I stated in the first sentence, I doubt the usefulness of classical MD for simulating crystallization of NaCl. Whatever I state after that applies to the case of trying it with classical MD nonetheless. Please read closely before trying to outwit however you find on this list. Second, as is cle

Re[2]: [gmx-users] RE: can gmx be used to simulation NaCl

2008-06-28 Thread Vitaly Chaban
Tsjerk, Well, the best way would be AIMD, no doubt. William, Look here http://www.mpibpc.mpg.de/groups/grubmueller/start/teaching/vorlesung_computerbiophysik_2004/p4/index.html for an example how freezing/melting of argon is processed by means of GROMACS. TW> Hi William, TW> I'm not very sure y

Re: [gmx-users] RE: can gmx be used to simulation NaCl

2008-06-28 Thread Tsjerk Wassenaar
Hi William, I'm not very sure you can simulate crystallization of salt with classical MD. In any case, the force field is not parameterized to reproduce crystallization or melting c.q. the melted state of NaCl. It's therefore unlikely that it will produce meaningful results. The best approach :) w

[gmx-users] RE: can gmx be used to simulation NaCl

2008-06-27 Thread Vitaly Chaban
I see no problems to use gromacs for it. You make find the parameters in /top/ions.itp (include ions.itp to your topology) in your gromacs directory. Then you can use 'genconf' to create a system of the desired size. > hi gmx users, > Can Gromacs be used to simulate NaCl crystallization a