From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jun 12 2007 - 15:28:48 CDT
Hi Madhu,
the margin shouldn't have any physical effect on the simulation -- all
that it does is change how namd splits up the system into patches for
the simulation. However, if you're doing an NPT simulation, you should
not expect to get identical results between runs -- please see the
discussion of the seed keyword at
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node26.html.
The margin keyword itself is discussed at
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node26.html#5124
Peter
M. Madhu wrote:
> Hi NAMD users,
>
> During my TMD simulation (NPT) in a lipid bilayer, I get the following fatal error.
> ================================
> FATAL ERROR: Bad global exclusion count!
>
> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Bad global exclusion count!
>
> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
> ================================
>
> However, It works without any warning If use a margin value greater than 50.
> I tried with margin 50 and margin100. According to NAMD user's guide margin
> parameter will not change the physical results of the simulation. But the final
> energies obtained with margin 50 and 100 are different.
>
> Cany anyone tell me what exactly this parameter is doing in the simulation?
> How this parameter retains the physical results with different margin values,
> though the final energies are different?
> Whether a large margin value (eg: 50) causes any adverse effects in the simulation.
>
> Thanks,
> Madhu
>
> _________________________________________________________________
> Catch the cricket action with MSN!
> http://content.msn.co.in/Sports/Cricket/Default.aspx
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:50 CST