RE:

From: Anna James (annajamesmatrix_at_hotmail.com)
Date: Tue Aug 16 2011 - 08:48:51 CDT

Wow
That was a quick reply.
I am not sure If I understand how to use multiple segments and file.When It comes to solvating in vmd using non standard solvents, I always use the following script :

http://www.ks.uiuc.edu/Research/namd/2.8/ug/node19.html

Can you be a bit more specific on your suggestion ?

Anna James Vaughan
Leeds

> Date: Tue, 16 Aug 2011 09:43:00 -0400
> Subject: Re: namd-l:
> From: akohlmey_at_gmail.com
> To: annajamesmatrix_at_hotmail.com
> CC: namd-l_at_ks.uiuc.edu
>
> On Tue, Aug 16, 2011 at 9:38 AM, Anna James <annajamesmatrix_at_hotmail.com> wrote:
> > Hello NAMD Experts
> >
> >
> > I have a query about setting up a PBC unit.Unfortunately I am working with a
> > large Globular Protein,the extent of which is around 90A in all the three
> > X,Y Z axes that would mean My PBC Unit has to be larger than it to encompass
> > the whole protein. I Created a Methanol Box of 100*100*100 A and filled it
> > up with Methanol molecules as the per the density of Methanol .The number of
> > Molecules exceeded 35000 and VMD/PSFGEN cannot process PDBs that have
> > residues more than 9999.
>
> just use multiple segments (and multiple files). the numbers
> can start fresh for each segment.
>
> axel.
>
> >
> > I am sure lot of people would have worked with PBC units as large as 90A
> > ,What is the way to go about solvating them ?Do we have to compromise on the
> > number of Methanol Molecules while setting up the system?
> >
> > I am using the following parameters :
> >
> > exclude scaled1-4
> > 1-4scaling 1.0
> > cutoff 12.0
> > switching on
> > switchdist 10.0
> > pairlistdist 14.0
> > timestep 2.0
> > rigidBonds all
> > nonbondedFreq 1 .
> >
> > Looking at the above parameters, What would be the safe distance between the
> > images while setting up PBC units?
> > Are the above parameters good enough ?
> >
> >
> > In anticipation of an encouraging reply
> >
> >
> > Anna James Vaughan
> > Leeds
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
                                               

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