[gmx-users] flexible spc water model

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> 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.
> 

Well, hopefully someone has proven that this should be possible.  SPC was 
designed to be rigid, not flexible:

http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html

-Justin

> 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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> 
> 
> 

-- 
========================================

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

========================================