[gmx-users] on NVE and pressure

[andrew stelzer]

sure, what room number in Palmer?

Andrew Stelzer
The University of Michigan
Chemical Biology Doctoral Program
Department of Chemistry &
Biophysics Research Division
900 N. University
Ann Arbor, MI 48109



On Apr 16, 2007, at 9:33 AM, lorix wrote:

>
> The goal of mine is to see whether I can simulate a large  
> conformational change on an protein.
> A relative movement of one part respect another one, a rearrangment  
> of on enzyme inactive state to its active one.
> When I started more than I year ago I thought this was the MD  
> framework.
> I am modifing the inactive state, present in a crystallographic  
> structure, in a way that would lead to the conformational change  
> and then simulating as accurate as possible.
> I guess that what I am interesting in is the conformation evolution  
> of the protein system rather than monitoring parameters. For what I  
> can understand this evolution is deterministically correlated with  
> the atom velocities. So far I appreciated how trajectories changed  
> depending on the initial conditions and on the used settings and  
> parameters.
>
> Statistics over 624001 steps [ 114.0000 thru 738.0000 ps ], 1 data  
> sets
>
> Energy                      Average       RMSD     Fluct.       
> Drift  Tot-Drift
> ---------------------------------------------------------------------- 
> ---------
> Total-Energy                -464122    10572.6          0    
> -58.7363   -36651.5
>
> The drift seems to me quite large compare to other simulations.
> Shouldn't the energy be constant in NVE?
>
>
> thanks for helping,
> loris....
>
>
>
>
> Berk Hess wrote:
>
>>
>>
>>
>>> From: lorix <Loris.Moretti at pharm.unige.ch>
>>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> Subject: Re: [gmx-users] on NVE and pressure
>>> Date: Mon, 16 Apr 2007 12:25:15 +0200
>>>
>>> Hi Berk and Jelger,
>>>
>>> Thanks for your comments...
>>> Yes I equilibrated the system with Berendsen thermostat and  
>>> barostat for 100ps and 200 ps and then switched them off.
>>> I thought that the coupling could have an influence in the final  
>>> trajectory, because of the atom velocities scaling (?).
>>> Why does not make sense to run NVE after NPT?
>>
>>
>> You don't specify what your goals are, so I have to guess what you  
>> want.
>>
>> MD is inherently chaotic and velocity correlations decay quickly,
>> so using NVE does, in general, not provide "better" velocities  
>> than NVT.
>> NVT is usually what you want when your system is in thermal  
>> equilibrium.
>> Only when you have energy dissipation after an event which takes  
>> your system
>> out of thermal equilibrium, i.e. pumps energy into the system,
>> it makes sense to use NVE.
>> However, when you equilibrate using NVT, this energy will already  
>> be dissipated.
>>
>>>
>>> The two systems (15000 and 40000 atoms) I am simulating at NVE  
>>> both show increasing total energy:
>>>
>>> The first system had -154442 kJ mol^-1 as average for the 7-207  
>>> psec NPT equilibration and -168837 kJ mol^-1 as average value for  
>>> 1500-2000 ps of NVE.
>>>
>>> The second system had -445679 kJ mol^-1 as average for the 14-114  
>>> psec NPT equilibration and -465630 kJ mol^-1 as average for the  
>>> 300-600 ps of NVE equilibration.
>>
>>
>> For energy conservation you should not look at the average energy,
>> but the energy drift during your NVE simulation.
>>
>> Berk.
>>
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