[gmx-users] NPT or NVT

[Riccardo Concu]

Hi Gianluca,
I'm not working with proteins, my bad I don't tell you, but BTW I will try 
with your suggestion.
Thanks,
Riccardo

-----Original Message----- 
From: Gianluca Interlandi
Sent: Friday, January 03, 2014 7:50 PM
To: gmx-users at gromacs.org ; jalemkul at vt.edu
Subject: Re: [gmx-users] NPT or NVT

My advise would be to apply harmonic constraints to the heavy atoms of the
protein and run 200 ps of NPT at the higher temperature. Then release the
constraints.

Gianluca

On Thu, 2 Jan 2014, Justin Lemkul wrote:

>
>
> On 1/2/14, 5:34 AM, Riccardo Concu wrote:
>> Dear all, I?ve a doubt/question. I ran a long simulation of my system
> (100ns)
>> at 298K. Now I want to see the effect of the T on my system and I want to
> run
>> a 20ns simulation at 350K and 400K, now my question is: Do I have to run
> this
>> simulation under the NPT condition or under the NVT (using an annealing 
>> for
>> example?). I?m trying to run the simulation at 350K using the final gro 
>> of
> my
>> simulation but the system is very unstable and finishes due to too many
> lincs
>> warning.
>
> You will need to thoroughly re-equilibrate the system under whatever new 
> conditions you impose.  Annealing may be useful.  Higher temperatures also 
> may require a shorter time step to be stable.  As for ensemble, NVT will 
> be more stable, but you need to decide what to use based on what is 
> relevant, not what may happen to "just work."  You can make NPT work, but 
> proper preparation and input settings will be required.
>
> -Justin
>
> -- 
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
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-----------------------------------------------------
Gianluca Interlandi, PhD gianluca at u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
                     http://healthynaturalbaby.org
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