[CP2K:6060] MM in CP2K

Rolf David rolf.d... at gmail.com
Thu Feb 5 14:19:36 UTC 2015

I'll try. I need to take one faulty AA and put it in TIP3P water.

I think the problem is the H of the backbone (linked to the nitrogen 
backbone) in my AA (homemade parameters made with MCPB) is negative. So 
there should be a attraction between this H and one from the TIP3P solvent. 
But this didn't occurred in the amber MD. The H is around 3/4A from any 
other Hs from solvent (and no H-bonding with a O from solvent).
In ambermd when the H come too close (ie 2.5/2 A), there is a repulsion so 
they don't get dangerously close and eventually merge like in CP2K.

>From my point of view it's like the H from TIP3P doesn't exist (just a 
charge, there is no vdw for H in TP3P), because geom wrong is from the H 
from the backbone and the O from water.

So possibilities:
I redo the charge by restraint the backbone charge in my metal center from 
standard amber (H positive) (but why it worked in amber md and not cp2k ?)
I put a fictious very weak wdv for the HW from TIP3P to avoid 
'collision/merging' (again why ambermd and not cp2k ?)

I guess my param are wrong but same question why ambermd is working and not 
cp2k. Maybe it's in the amber side and cp2k is working as attended.

I'll try to strat from different points from the amberMD simulation 
production run, to see if eventually there is a merging in all cp2k 

I'll keep you posted (and I'm open for more ideas !) for the small system.

On Thursday, February 5, 2015 at 2:21:17 PM UTC+1, Teo wrote:
> Can you reproduce that with a small system (i.e. ~ 30 atoms) ?
> On 05 Feb 2015, at 12:48, Rolf David <rolf... at gmail.com <javascript:>> 
> wrote:
> Hi everyone. 
> I have a system (protein in a water box) and I encoutered problems in MM 
> only (via FIST) in CP2K (periodic box)
> I first used xleap to prep my files, run a minimization, a heating, a 
> equilibration a production run (around 150ns). Everything was fine with 
> amber12 (pmemd)
> After I switched to CP2K (2.5.1) with FIST using amber restart, topology 
> parameters, I run into a problem around 600fs. 
> One H of the solvent (TIP3P water) slowly goes near and collides/merges 
> with a H from the backbone of my protein and so go to geom wrong, 
> emax_spline too small.
>  I checked FF_INFO and FF_PARAMETERS everything seems in order. When I do 
> the DO_NONBOND keyword to true, the merging didn't append (but other 
> problems).
> I wonder how CP2K handles VdW and Electrostatic. The Electrostatic seems 
> to win.
> Anybody have ideas ? Do you want more infos ?
> Thanks for every hints you can give me.
> Rolf
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