[gmx-users] flexible spc water model

Nilesh Dhumal ndhumal at andrew.cmu.edu
Mon Mar 28 14:29:23 CEST 2011


I want to calculate the vibrational spectra of water by fourier transfom
of velocity autocorrelation function. TO study stretching and bending
vibration I have to use spc flexible water model.

Nilesh

On Fri, March 25, 2011 12:02 pm, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> Hello,
>>
>>
>> I am want to use flexible spc water model for my simulation.
>>
>>
>
> Might I inquire as to why?  SPC was parameterized to be rigid, and as has
> been stated numerous times across the list, flexible water should not be
> used.
>
>> I define=-DFLEX_SPC in my mdp and mentioned  #include "spc.itp" in my
>> .top
>> file.
>>
>> Does it correct?
>>
>>
>
> Presumably.  Check the post-processed topology that grompp gives you (-pp
> argument).
>
> -Justin
>
>
>>
>> I am using gromacs 4.0.7 version.
>> Thanks
>>
>>
>> Nilesh
>>
>>
>>
>
> --
> ========================================
>
>
> 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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