Re: [gmx-users] SPC water model for CHARMM27FF

[Archana Sonawani-Jagtap]

Thanks Justin. Will try to use CHARMM36 with TIP3P watermodel.

On Sat, Oct 28, 2017 at 11:57 PM, Justin Lemkul  wrote:

>
>
> On 10/28/17 5:49 AM, Archana Sonawani-Jagtap wrote:
>
>> Dear all,
>>
>> I have used SPC water model with CHARMM27 forcrfield for performing 100ns
>> protein-DNA simulation instead of TIP3P. I wanted to know if SPC water
>> model can affect my simulation results in anyway considering many charged
>> residues.
>>
>
> Yes, it certainly is. CHARMM specifically balances water interactions
> assuming CHARMM-modified TIP3P (with LJ on H atoms) to target individual QM
> water interactions. If you change the water model, you potentially
> imbalance the entire force field. The water model should generally be
> viewed as an integral part of the force field, unless one does a complete
> validation that the change in water model does not negatively impact the
> target data (water interactions, hydration free energies, helix-coil
> equilibrium, etc).
>
> CHARMM36 is also superior to CHARMM27 and I recommend you use it instead,
> particularly if you care about subtle aspects of the DNA structure.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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-- 
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339
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Re: [gmx-users] SPC water model for CHARMM27FF

[Justin Lemkul]

On 10/28/17 5:49 AM, Archana Sonawani-Jagtap wrote:

Dear all,

I have used SPC water model with CHARMM27 forcrfield for performing 100ns
protein-DNA simulation instead of TIP3P. I wanted to know if SPC water
model can affect my simulation results in anyway considering many charged
residues.


Yes, it certainly is. CHARMM specifically balances water interactions 
assuming CHARMM-modified TIP3P (with LJ on H atoms) to target individual 
QM water interactions. If you change the water model, you potentially 
imbalance the entire force field. The water model should generally be 
viewed as an integral part of the force field, unless one does a 
complete validation that the change in water model does not negatively 
impact the target data (water interactions, hydration free energies, 
helix-coil equilibrium, etc).


CHARMM36 is also superior to CHARMM27 and I recommend you use it 
instead, particularly if you care about subtle aspects of the DNA structure.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] SPC water model for CHARMM27FF

[Archana Sonawani-Jagtap]

Dear all,

I have used SPC water model with CHARMM27 forcrfield for performing 100ns
protein-DNA simulation instead of TIP3P. I wanted to know if SPC water
model can affect my simulation results in anyway considering many charged
residues.

Please help me out.

Archana Jagtap
PhD student
India.
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