From: Andrea Holfelder (andreaholfelder_at_gmx.com)
Date: Thu Sep 01 2011 - 03:09:09 CDT
Thanks Johan
My PBC unit had the following stretch in dimension
-54 to 53 X direction == and I used Cell basis vector 1 107 0 0
-45 to 44 Y direction == and I used Cell basis vector 2 0 92 0
-34 to 64 Z direction == and I used cell basis vector 3 0 0 100
PME
PMEX 110
PMEY 95
PMEZ 105
and I used margin 2.5
,I was getting the error without using margin and when I used margin,it ran ,I was just wondering what possible effect this "margin" is having on my simulation.
----- Original Message -----
From: johan strumpfer
Sent: 09/01/11 11:05 AM
To: Andrea Holfelder
Subject: Re: namd-l: Margin Value in NAMD
Hi Andrea, Your understanding is not correct: From the namd user's guide (http://www.ks.uiuc.edu/Research/namd/2.8/ug/node39.html): margin $ <$ extra length in patch dimension (Å) $ >$ Acceptable Values: positive decimal Default Value: 0.0 Description: An internal tuning parameter used in determining the size of the cubes of space with which NAMD uses to partition the system. The value of this parameter will not change the physical results of the simulation. Unless you are very motivated to get the very best possible performance, just leave this value at the default. I.e. it has no bearing on the physics. It is only used in the computational parallelisation scheme. It sounds like you haven't set the size of your periodic cell correctly - check the basis vector sizes against the size of your water box. Cheers, Johan ------------------------------------------------------------------------------------------------------ Johan Strumpfer: johanstr_at_ks.uiuc.edu www.ks.uiuc.edu/~johanstr Theoretical and Computation
al Biophysics Group 3115 Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Urbana, IL 61801, USA ------------------------------------------------------------------------------------------------------ On Thu, Sep 1, 2011 at 12:57 AM, Andrea Holfelder <andreaholfelder_at_gmx.com> wrote: > Thanks Johan > > Should I then keep using Margin command ? > Is it good to keep the margin command ? > I am using Margin 2.5 when my Cell basis vector is around 100 in x y z > direction. > > From what I understand by ur explanation is that ,Margin value gives the pbc > unit flexibity by 2.5 units in each direction(x,y,z) to change and adapt to > new size. > Is it ? > > Is it physiologically relevant to use margin ? > > > What is the recommended value of margin when cell basis vector is aroun 100 > in x y z direction. > > > > ----- Original Message ----- > > From: johan strumpfer > > Sent: 09/01/11 09:26 AM > > To: Andrea Holfelder > > Subject: Re: namd-l: Margin Value in NAMD > > > Hi Andrea, > >!
The mar
gin helps determine which atoms are assigned to which computing > patches. The error you're getting from removing the patch command is > likely because your simulation is changing size, maybe as it adapts to > a different box size or pressure. > > Cheers, > Johan > > ------------------------------------------------------------------------------------------------------ > Johan Strumpfer: johanstr_at_ks.uiuc.edu > www.ks.uiuc.edu/~johanstr > Theoretical and Computational Biophysics Group > 3115 Beckman Institute > University of Illinois at Urbana-Champaign > 405 N. Mathews > Urbana, IL 61801, USA > ------------------------------------------------------------------------------------------------------ > > > > On Wed, Aug 31, 2011 at 10:42 PM, Andrea Holfelder > <andreaholfelder_at_gmx.com> wrote: >> I am not sure the importance of Margin value while running a PBC >> simulation. >> >> My cell basis vectors are around 100 for each of x y z and when I keep >> margin =2.5 the simulation runs quite welll but when I remove
the margin >> from the config file ,I get an error after some time into the simulation >> which says something like "the grid patch has become too small etc. etc. >> " >> >> >> What role is the Margin playing here? >> What does Margin do? >> >> > >
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