[gmx-users] DFLEXIBLE option

[Kavyashree M]

Thanks

With Regards
Kavya

On Tue, May 10, 2011 at 5:32 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Kavyashree M wrote:
>
>> Dear users,
>>
>>      I wanted to know when DEFINE = -DFLEXIBLE has to be used.
>> its given in the manual that it has to be used when we require flexible
>> water instead of rigid waters, so if I am using tip4p water model and
>> OPLSAA force field, and i use DFLEXIBLE option in EM and not in
>> position MD, is there anything wrong? Kindly clarify my confusion.
>>
>>
> Flexible water should be only really be used during EM and not MD.  All the
> water models included in Gromacs were designed to be rigid.  Using "define =
> -DFLEXIBLE" helps EM proceed a bit further, but is not appropriate for
> running MD.
>
> -Justin
>
>
>  Thanking you
>> With Regards
>> Kavya
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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