[gmx-users] NPT restarts without .edr, can the simulations be used anyway?

[Justin A. Lemkul]

Matteus Lindgren wrote:
> Hi all
> 
>  
> 
> I am new to gromacs and despite my efforts in reading tutorials, the 
> manual and this mailing list I managed to make errors when restarting 
> (continuing) some NPT MD simulations.
> 
> I have continued my simulation runs with grompp but with an mdp-file 
> lacking the tinit, init_step, unconstrained_start options. Also, I did 
> not supply an .edr file to grompp, just the previous .trr file.
> 
> The simulations are protein in explicit solvent simulations with 
> Parrinello-Rahman and nose-hoover PT control. Hydrogens are constrained 
> as well as the SPCE water molecule. They will be analyzed in terms of 
> solvent and protein dynamics and perhaps forces.
> 
>  
> 
> I guess the simulations can´t be used but perhaps you can give me some 
> insight into what effects the errors might have had.
> 
>  

At least with respect to the Nose-Hoover temperature coupling - Nose-Hoover 
relies on a "memory" of sorts, the rate of how the temperature is changing.  I 
don't know exactly what type of artefacts that might cause, but I am willing to 
bet that the coupling will be inconsistent if there is no evidence of how the 
temperature is changing.

For rigorous preservation of such coupling parameters, an .edr file is 
definitely necessary.

-Justin

> 
> Thank you
> 
>  
> 
> Matteus Lindgren
> 
> Graduate student
> 
>  
> 
> Department of Chemistry
> Umeå University
> SE-901 87 Umeå, Sweden
> Tel: +46 (0)90 786 53 68
> e-mail: matteus.lindgren at chem.umu.se <mailto:barbara.addario at chem.umu.se>
> 
>  
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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