On 12/4/17 7:47 AM, Daniel Bauer wrote:
Hello Justin,
Thanks for your response. I was under the assumption that entries in [
pairtypes ] are the ones that override standard LJ interactions derived
by pairgen. I now know this is a different section.
From what you are saying I come to the conclusion that the POT O
interaction in charmm36 for gromacs have no custom potential but are
derived via combination rules (as they are in namd). Nevertheless, the
numbers still dont seem to match:
Since we can ignore 1-4 Interactions in charmm36 as well as gromacs for
POT-O, the resulting parameters from the namd version are:
sig = 0.3463750 nm; eps=0.42750571533 kJ/mol
Can you please share the source of these parameters? There should be no
"NAMD version" of anything. The force field files that you should be
using are just the CHARMM distribution. The GROMACS port of CHARMM36
comes directly from those files. There is no official NBFIX for POT-O
(yet, we do have one but it's not in the official distribution) so the
combination rules should prevail.
-Justin
However, combining the entries for O and POT in the atomtypes section of
the gromacs version i get something different:
[ atomtypes ]
O 8 15.999000 0.000 A 0.302905564168 0.50208
POT 19 39.098300 0.000 A 0.314264522824 0.36401
=======================================
sig = 0.308585043 nm; eps=0.42750689 kJ/mol
Again, the epsilon value is matching the namd version while sigma is
still off by about 0.4 A.
If my conversion of the namd parameters and combination rules are
correct, this would be a problem. The different position of the energy
minimum results in a potential energy difference of around 7 kJ/mol for
a distance of 0.29 nm (typical distance for POT-O in the selectivity
filter of potassium channels, see attached image).
Can you give me a source where I can read up on why the values for sigma
and epsilon in gromacs are the way they are? It must be more than a
direct conversion of the numbers from kcal to kJ. Or did I again made a
mistake or took the wrong numbers?
Best regards,
Daniel
On 12/03/2017 11:23 PM, Justin Lemkul wrote:
On 12/3/17 4:18 PM, Daniel Bauer wrote:
Hello,
I compared the LJ parameters for the interaction Potassium - backbone
carbonyl oxygen for CHARMM36 between the Gromacs and NAMD version of the
forcefield. I found different numbers for the sigma value i cannot
explain to myself:
The stock charmm36 implementation has the following LJ parameters for
potassium and oxygen:
; atom Emin (kcal/mol) Rmin/2 (A)
POT 0.087 1.76375
O 0.120 1.7
Converting the above values to units used in gromacs (kJ/mol and nm) and
applying standard combination rules this should give the following
nonbonded energy parameters:
[ pairtypes]
; sig = (Rmin,i/2 + Rmin,j/2)/10
; eps = sqrt(Emin,i * Emin,j) * 5.184 kcal/kJ
; i j func sig (nm) eps (kj/mol)
O POT 1 0.346 0.4275
However, the actual entry for the interaction in GROMACS/charmm36 has
the energy minimum at a much smaller distance (epsilon is on the point
though!)
; i j func sig (nm) eps (kJ/mol)
O POT 1 0.282 0.4275
Can somebody tell me the reason for this huge difference? Is there an
error in my calculation? I am trying to convert an NBFIX applied to this
specific interaction to gromacs. However, I am not sure how to proceed
without doing the reparametrization in gromacs again, because the stock
values differ that much.
This is actually a value that isn't used. [pairtypes] are for 1-4
interactions, which can never occur between a K+ ion and a carbonyl O.
The inclusion in the list is just because it's really hard to tell our
conversion program to exclude some massive list of impossible
interactions. So they get generated.
But to your point, you're missing a critical point of the CHARMM
parameter format. The full NONBonded parameter entry in
par_all36m_prot.prm for carbonyl O is:
O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000
The last fields are epsilon and Rmin/2 when that atom type is used in
a 1-4 interaction. So -0.12/1.7 is for the normal nonbonded
interaction, -0.12/1.4 is for any 1-4 involving O.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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