Hi Lucia,
I’m not sure what you are trying to do with ‘--centering 0’. This should be considered an expert setting and is only used in special circumstances. Also, are you using periodic or non-periodic 3D-RISM. Your full command line would help.
The 3D-RISM solvation grid starts at (0,0,0) and goes to (solvbox_x, solvbox_y, solvbox_z). With ‘—centering 1’ the solute center-of-mass is move to the center of this box for the 3D-RISM calculation and then moved back to its original location. Any output grids are appropriately translated to the original location of the solute. This is almost always what you want.
‘—centering 0’ gives you the option to manually place the solute in the solvation box. The solvation grid is still from (0,0,0) and to (solvbox_x, solvbox_y, solvbox_z) but the position of the solute is not changed from its original location. You, as the user, need to provide an input file with the solute positioned exactly as you want with the knowledge of where the solvent grid will be.
The second most popular option is ‘—centering 2’, which translates the center-of-geometery of the solute. This is used for minimization where the center-of-geometry is constant instead of the center-of-mass.
HTH,
Tyler
> On Apr 20, 2017, at 10:05 AM, Lucia Fusani <lucia.x.fusani.gsk.com> wrote:
>
>
> Hi,
>
>
> I am using rism3d.snglpnt (in Amber 16) and when I specify the option
> “--centering 0” as well as the grid size and grid points (--solvbox and –ng)
> I get an unexpected results. See attached picture. I obtained the same
> results with Amber12.
>
> What am I doing wrong and what can I do to fix that? The reason why I want
> centering 0 is because I want to be able to decide the origin of the grid
> that is not possible in any other cases. Any suggestions?
>
>
> Many thanks
>
>
> Kind Regards,
>
> Lucia
>
>
> Lucia Fusani
>
> Industrial PhD Student
>
> Complementary Worker on Assignment at GSK
>
> Molecular Design UK
>
> R&D Platform Technology & Science
>
>
> GSK Medicines Research Centre
>
> Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
>
> Email [1]Lucia.x.Fusani.gsk.com
>
>
> [2]gsk.com | [3]Twitter | [4]YouTube | [5]Facebook | [6]Flickr
>
>
> cid:image001.png.01D0FF8F.1ACF64F0
>
> _________________________________________________________________
>
> This e-mail was sent by GlaxoSmithKline Services Unlimited
> (registered in England and Wales No. 1047315), which is a
> member of the GlaxoSmithKline group of companies. The
> registered address of GlaxoSmithKline Services Unlimited
> is 980 Great West Road, Brentford, Middlesex TW8 9GS.
>
> GSK monitors email communications sent to and from GSK in order to protect
> GSK, our employees, customers, suppliers and business partners, from cyber
> threats and loss of GSK Information. GSK monitoring is conducted with
> appropriate confidentiality controls and in accordance with local laws and
> after appropriate consultation.
>
> References
>
> 1. mailto:Lucia.x.Fusani.gsk.com
> 2. http://www.gsk.com/
> 3. http://twitter.com/GSK
> 4. http://www.youtube.com/user/gskvision
> 5. http://www.facebook.com/glaxosmithkline
> 6. http://www.flickr.com/photos/glaxosmithkline
> <image001.png><centering0.jpeg>_______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 20 2017 - 11:30:04 PDT
