Ozge Engin wrote:
Hi all,
I have been trying to calculate the PMF of two NA+ ions in explicit bulk
water. First, I tried to calculate the mean force between the two ions
at a distance of 0.48 nm, which is big enough than the diameter of the
ions. I first energy minimized the system with the script below, but it
did not converge. After that, I removed one of the ions, and tried
again, it did not work again.
I am using ffG43a1 ff, and checked whether I used the correct naming for
the ion: Everything seems to be OK.
Irrelevant. If naming were an issue, grompp would have failed with a fatal
error.
I could not attach the initial coordinate file due to the limited size.
If you want I can also sent it to you as well.
*Script: *
title = Minimization
cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 30000
nstlist = 10
ns_type = grid
rlist = 1.0
vdwtype = cut-off
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.4
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 100.0
emstep = 0.01
*Output*:
Steepest Descents converged to machine precision in 36 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -1.0409969e+05
Maximum force = 9.6685031e+04 on atom 294
Norm of force = 1.4924829e+03
What may be the problem?
Not a clue. What is atom 294? Look at the output - what are the other nearby
atoms that could be causing the excessive force?
-Justin
Best Regards
--
Ozge Engin
★☆
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
