Hello,<br><br>Yes, I have come across that but If the temperature is below<br>the boiling point its fine. But if it crosses the boiling temperature<br>in order keep the water as liquid isnt it necessary to increase the<br>
pressure. I understand that the water models do not exactly predict <br>the transition temperature. So in what way does this behaviour of water <br>effect the simulation of a protein?<br><br>Thank you<br>With Regards<br>kavya<br>
<br><div class="gmail_quote">On Mon, Oct 17, 2011 at 5:13 PM, bipin singh <span dir="ltr"><<a href="mailto:bipinelmat@gmail.com">bipinelmat@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Well,as I found in literatures people have used same( 1 atm) pressure<br>
at high temperature simulations(NPT simulations).<br>
with different water models.As most of the force field parameters are<br>
determined generally at 300K and 1 atm.<br>
What would be the the possible drawbacks of using the same pressure(or<br>
even high pressure) at different temperatures(300K-400K ranges) for a<br>
given force field.<br>
<div><div></div><div class="h5"><br>
On Mon, Oct 17, 2011 at 17:04, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
><br>
><br>
> Kavyashree M wrote:<br>
>><br>
>> Thank you,<br>
>><br>
>> What about the pressure that need to be used at that temperature<br>
>> (for a system of a protein in tip4p water)<br>
>><br>
><br>
> The set pressure should reflect whatever system you are trying to model.<br>
><br>
> -Justin<br>
><br>
>> Thank you<br>
>> With Regards<br>
>> Kavya<br>
>><br>
>> On Mon, Oct 17, 2011 at 3:29 PM, bipin singh <<a href="mailto:bipinelmat@gmail.com">bipinelmat@gmail.com</a><br>
>> <mailto:<a href="mailto:bipinelmat@gmail.com">bipinelmat@gmail.com</a>>> wrote:<br>
>><br>
>> As far as I know we do energy minimization at room temperature only.<br>
>> Only during equilibration<br>
>> (NVT and NPT) we use high temperature for maintaining proper density<br>
>> before starting the final production run.<br>
>><br>
>> On Mon, Oct 17, 2011 at 15:15, Kavyashree M <<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a><br>
>> <mailto:<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>>> wrote:<br>
>> > Dear users,<br>
>> ><br>
>> > For simulating a protein at high temperature (more than 300K,<br>
>> > less than 400K) using OPLSAA forcefield, what are the parameters<br>
>> > other than Temperature that need to be taken care of?<br>
>> > Does the energy minimization step also needs to be done at high<br>
>> > temperature? (here my aim is not to simulate an unfolding event)<br>
>> > I have a reference -<br>
>> > Biophysical Journal Volume 94 June 2008 4444–4453<br>
>> ><br>
>> > Any other references or suggestions will be helpful.<br>
>> ><br>
>> > Thanking you<br>
>> > With Regards<br>
>> > M. Kavyashree<br>
>> ><br>
>> ><br>
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><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
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> Department of Biochemistry<br>
> Virginia Tech<br>
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