Re: Cascade MDFF

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Thu Mar 09 2017 - 10:53:42 CST

Unfortunately if it is non-orthogonal, you will have to use something other
than VMD. Chimera's Volume Filter may work, but I am not 100% sure.

On Thu, Mar 9, 2017 at 10:29 AM Luba Simhaev <luba.simhaev0703_at_gmail.com>
wrote:

> Thank you for the reply.
> I'm running the volutil on the original density map.
> If the map is non-orthogonal, which command should I use?
>
> Thanks
> Luba
>
> On Thu, Mar 9, 2017 at 4:25 PM, Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu>
> wrote:
>
> First, make sure you are running volutil on the original density map, and
> not the potential you get from the griddx command. Second, the volutil
> command won't work properly if your map is non-orthogonal.
>
>
> On Thu, Mar 9, 2017 at 2:38 AM Luba Simhaev <luba.simhaev0703_at_gmail.com>
> wrote:
>
> Hi all NAMD users,
> I'm trying to run cascade MDFF. For this purpose I have to generate maps
> with lower resolution from the original map with the volutil command in vmd
> using various sigma values. If I understand correctly, in case of sigma=0
> it should return the original potential map, and and in case of sigma>0 ,
> it should returns smoothened maps (with more density regions).
> Actually, the situation is opposite: when I increasing the sigma value
> there are less density regions.
> Can anyone please help me to solve it?
>
> Thanks,
> Luba
>
> --
>
> *Luba Simhaev*
>
> *PhD Candidate*
>
> *Chemistry **Department*
>
> *Bar-Ilan University*
>
>
>
>
> --
>
> *Luba Simhaev*
>
> *PhD Candidate*
>
> *Chemistry **Department*
>
> *Bar-Ilan University*
>

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