On 11/16/12 3:43 PM, Yao Yao wrote:
Hi Gmxers,
I am doing a protein NMA with the mdp file like,
===========================================
define = -DEFLEXIBLE
constraints = none
integrator = nm ;
emtol = 0.00001
emstep = 0.1
nsteps = 4000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 0 ; Frequency to update the neighbor list and long range
forces
ns_type = simple ; Method to determine neighbor list (simple,
grid)
;vdwtype = switch
vdwtype = cut-off
rlist = 0.0 ; Cut-off for making neighbor list (short range forces)
;coulombtype = PME-switch ; Treatment of long range electrostatic
interactions
coulombtype = cut-off
;rcoulomb = 1.2 ; Short-range electrostatic cut-off
rcoulomb = 0.0
;rvdw = 1.2 ; Short-range Van der Waals cut-off
rvdw = 0.0
pme_order = 4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
optimize_fft = yes
pbc = no
=====================================================
However, it shows
"Fatal error:
Constraints present with Normal Mode Analysis, this combination is not
supported"
Since I put "Constaints" none, I really do not get it. Can someone help me?
The problem is a typo. You've set "-DEFLEXIBLE" instead of "-DFLEXIBLE" so
rather than having flexible water as intended, you've got rigid water via the
SETTLE algorithm, and constraints are still present.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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/Support/Mailing_Lists/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/Support/Mailing_Lists
