LES is an advanced sampling technique. Make sure before you use it
that you already have a strong knowledge of basic MD, and that your
system is already behaving well in standard simulations.
I worry that using Na+ ions in vacuum will have problems, and there
may be other issues to deal with that are not directly related to LES.
On Tue, Jun 26, 2012 at 8:29 AM, Sajeewa Pemasinghe <sajeewasp.gmail.com> wrote:
> Hi,
>
>>>>>>>Message contents removed at request of author Jun-26-2012.
>
>
> On Tue, Jun 26, 2012 at 5:49 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> it's hard to help without knowing more about what you are doing. for
>> example, I don't understand the solvateshell usage if you already have
>> a periodic box. did you use solvent in the box?
>> try to explain the steps that you took to build, equilibrate and run
>> the system. was the system equilibrated and run without LES prior to
>> making copies? give us the input file for the production run that has
>> problems. did you carefully look at the output file to check the
>> stability of the energy and temperature? make sure you do careful
>> analysis- follow the tutorials if you haven't already.
>>
>> On Mon, Jun 25, 2012 at 12:30 PM, Sajeewa Pemasinghe
>> <sajeewasp.gmail.com> wrote:
>> > Hi all,
>> >
>>>>>>>Message contents removed at request of author Jun-26-2012.
>>
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Received on Tue Jun 26 2012 - 06:30:03 PDT
