[gmx-users] when gen_vel should be "no"

Florian Dommert dommert at fias.uni-frankfurt.de
Wed Aug 27 13:36:37 CEST 2008

On 27.08.2008, at 11:14, sarbani chattopadhyay wrote:

> hi,
>   I want to know that in what situation does the  initial velocity  
> to the  starting structure is to
> be kept at zero.
> thanks in advance
> sarbani


I think generating no initial vel. prevents introducing an artificial  
current into the system. This does not matter if you are only dealing  
with uncharged molecules( because the current always be zero). However  
if you simulate a system full of charged molecules, this affects the  
analysis of the data. For example calculation of the dielectric  
constant of a system with charged molecules can only be done by  
straightforward averaging if the current at the beginning of the  
simulation is zero, otherwise this approach fails.

Best Regards


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Florian Dommert

Computational and Theoretical Softmatter & Biophysics group

Frankfurt Institute for Advanced Studies
Johann-Wolfgang-Goethe University

Ruth-Moufang-Str. 1
60438 Frankfurt am Main

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EMail: dommert at fias.uni-frankfurt.de
Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert

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