Hi
Several comments.
Never run the WHOLE set of simulations before you are satisfied with the
overlap. Just run 3 or 4 windows and then see if you need to change
something before going further.
As for your qeustions:
Is that sufficient overlap? If it is not, do I need to reduce the spacing
or increase the force constant to get better overlap?
You do not show the overlap, so it is hard to tell you, but my guess
from your first figure is that no, it is not enough. By the way, if you
want to increase overlap, you need either a closer spacing and/or a
LOWER force constant(not increased!).
PLEASE add ig=-1 to your mdin !
As for your coordinate, it is NEVER a good idea to use just one distance
for a reaction. Look at published work on this, and you will see that
peopel tend to use a reaction coordinate that has RC=distance(bond being
broken) - distance(bond being made)
That produced much more stable surfaces.
adrian
On 10/23/15 7:56 AM, Mahmood Jasim wrote:
> Hi AMBER users,
>
> I am trying to simulate a reaction involving the formation of a covalent
> bond using umbrella sampling combine with QM treatment of the reaction
> atoms. I have the SG atom of a cysteine residue attacking an electrophilc
> carbon on a ligand. The distance between these 2 atoms is the reaction
> coordinate. The windows of umbrella sampling are spaced 0.3 Angstrom apart.
> The restraint file looks like this:
>
> #
> # 123 CYM SG 432 UNK C1 3.43
> &rst
> ixpk= 0, nxpk= 0, iat=1937,6803, r1= 2.93, r2= 3.43, r3= 3.43, r4= 3.93,
> rk2=0.0, rk3=100.0, ir6=1, ialtd=0,
> &end
>
> and the md.in file looks like this:
>
> &cntrl
> imin = 0,
> irest = 1,
> ntx = 7,
> ntb = 2,
> cut = 12,
> ntr = 0,
> ntc = 1,
> ntf = 1,
> igb = 0
> ntp = 1
> tempi = 300.0,
> temp0 = 300.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim =10000, dt = 0.001
> ntpr = 1000, ntwx = 1000, ntwr = 1000, nmropt = 1,
> ifqnt=1,
> /
>
>
> &qmmm
>
> qmmask =
> '.1934-1937,6794-6848',
> qmcharge =
> 0,
> qm_theory =
> 'PM3',
> qmcut =
> 12.0,
> /
> &wt type='DUMPFREQ', istep1=100,/
> &wt type='END' /
> DISANG=RST-1.dist
> LISTOUT=POUT
> DUMPAVE=DIST_1.dat
>
> The run was able to simulate the formation of the bond at the end and the
> next graph represents the values of the coordinates across the windows.
> [image: Inline images 1]
>
> Is that sufficient overlap? If it is not, do I need to reduce the spacing
> or increase the force constant to get better overlap?
>
> I used the WHAM code by Alan Grossfieldto calculate PMF with this command:
>
> wham 1.59 3.73 70 0.00001 300 0 meta.dat result.dat
>
> and this was the meta.dat file:
>
> DIST_1.dat 3.43 200
> DIST_2.dat 3.13 200
> DIST_3.dat 2.83 200
> DIST_4.dat 2.53 200
> DIST_5.dat 2.23 200
> DIST_5.dat 1.93 200
> DIST_7.dat 1.63 200
>
> and the histogram I am getting looks like:
>
> [image: Inline images 2]
>
> I was expecting the histogram to look different, the PMF to go higher and
> then decreases as it approcahes the products. If I managed to improve the
> overlapping, will this change the histogrm?
>
> Many thanks,
> Mahmood Jasim
> Aston University
> UK
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Fri Oct 23 2015 - 07:00:03 PDT
