Subject: advice on results ; X-PLOR parameter files for NaCl

From: Eugene Leitl <[email-masked]>
Date: Sun, 28 Jun 1998 18:44:43 +0400 (MSD)

Dear CCLers,

as part of my magistrate work I've made a number of MD simulations of
solvated biopolymers. Though both results and the manner of
presentation (beamer, movies, etc.) were well accepted locally, I 
am by no means certain that the results are not bogus. Can you advise?

Polyelectrolyte part:

I made fully charged polylysin (33mer and beyond, no hydrogens) with 
X-PLOR, and computed a few 10 ps worth of minimization and dynamics
(Helmut Heller's EGO with FAMUSAMM electrostatics).

As to be expected, in vacuo the equilibrium conformation is a string under
tension. (Structure generated by Axel Br"unger's X-PLOR's standard
peptide generation script heated spontaneously to 5-6 kK, after a few 
ps of minimization the system held the target 300 K stably, however).

After adding chlorides as counterions, and a few ps of minimization
dynamics the counterions are captured quantitatively, and initiate a
rapid compactisation of the polylysin into a random coil, crosslinked
by chloride ionic bridges. Each chloride acted as a coordination
nucleus for 2-3 -NH3+ groups. The equilibrium conformation did not
relaxate noticeably after having been subjected to solvatation
(TIPS3P; Helmut Grubm"uller's Solvate 1.0) within 20-30 ps. Solvated 
initial conformation in the beginning showed similiar dynamics,
however vastly inhibited though charge shielding and viscous
drag. (Due to lack of time and system size the results are very
preliminary).

To this part, I have the following questions. I used the following
parameter files for NaCl, which the original author deemed
unvalidated, and possibly unreliable.

parameter:
NONBonded  NAI     0.026    1.470       0.026    1.470    
NONBonded  CLI     0.26     1.835       0.26     1.835   

topology:
MASS   NAI   22.99000
MASS   CLI   35.45000
RESIdue INA
GROUp ATOM NA   TYPE=NAI   CHARge=  1.000  END
END
RESIdue ICL
 GROUp ATOM CL   TYPE=CLI   CHARge= -1.000  END
END

However, another source suggested the following parameters for Cl:
NONBONDED LC 0.0430 3.3676 0.0430 3.3676

(topo the same, hence omitted).

Which parameters are correct? (the difference in the values seem to indicate 
there is either no consensus, or one/both of these sets is/are
bogus). Are there any canonical, validated ones out there? Is there a 
depository for param/topo files somewhere to be found?

Since we are at that, how _does_ one derive parameter files? Unless
this is a real black art, I'd be thankful for any references. (Having
to rely on opaque semiempirical force fields is bad enough, but
feeding them with opaque ad hoc parameters of dubitable lineage 
is even worse).

[ second part on questions on phospholipid modelling now omitted for brevity ]

Thanks!

Regards,
Eugene Leitl