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

Matteus Lindgren matteus.lindgren at chem.umu.se
Fri Aug 29 13:45:47 CEST 2008

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.


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:  <mailto:barbara.addario at chem.umu.se> matteus.lindgren at chem.umu.se


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