[gmx-users] flexible spc water model

[Mark Abraham]

On 28/03/2011 11:29 PM, 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.

You probably should to use a flexible water model, but making flexible a 
model that was not designed to be flexible is not the best possible 
approach. Look in the literature for water models that were parametrized 
to be flexible, and preferably ones that are already known to reproduce 
such properties.

Mark

> 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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>