nahren manuel wrote:
Dear Gromacs Users,
I am trying to study ligand unbinding adopting Umbrella sampling (using
Gmx 4.5.3). during my initial pull to generate configurations for
umbrella windows I have pulled in the -Z direction,
@ s0 legend "0 Z"
@ s1 legend "1 dZ"
0.0000 7.37361 -0.33625
0.0200 7.37377 -0.33631
0.0400 7.37404 -0.33637
0.0600 7.3744 -0.33643
0.0800 7.37473 -0.33649
.
.
.
.
321.0800 7.37523 -1.29949
321.1000 7.37442 -1.29955
321.1200 7.37374 -1.29961
321.1400 7.37355 -1.29967
321.1600 7.37404 -1.29973
321.1800 7.37491 -1.29979
321.2000 7.3757 -1.29985
321.2200 7.37608 -1.29991
321.2400 7.37595 -1.29997
321.2600 7.37518 -1.30003
321.2800 7.37395 -1.30009
.
.
.(so on)
Now when I ran simulations in each umbrella windows, the PMF energies
are in negative. My guess is that this is due to my initial setup, or
is there something seriously wrong. And if i am right I should get the
correct PMF by taking the negative of this PMF (or is it)??
So your PMF is negative, why is that a problem? A negative binding energy
indicates favorability of binding.
-Justin
-----
; Pull code (pulling simulation)
pull = constraint
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = Protein
pull_group1 = MAL
pull_rate1 = 0.005 ;
pull_k1 = 1000 ; kJ mol^-1 nm^-2
pull_nstxout = 500 ; every 1 ps
pull_nstfout = 500 ; every 1 ps
-----
; Pull code (Umbrella simulation)
pull = umbrella
pull_geometry = distance ;
pull_dim = Y Y Y
pull_start = yes ;
pull_ngroups = 1
pull_group0 = Protein
pull_group1 = MAL
pull_rate1 = 0.000 ;
pull_k1 = 1000 ; kJ mol^-1 nm^-2
pull_nstxout = 500 ; every 1 ps
pull_nstfout = 500 ; every 1 ps
Best,
nahren
--
========================================
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 gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
