On 3/12/13 7:45 AM, raghav singh wrote:
Hello Fellow Users,
I have a doubt about the mdp option in case of constant velocity pulling /
Umbrella pulling simulation.
pull = umbrella
pull_geometry = distance ; simple distance increase
pull_dim = N N Y
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = Chain_B
pull_group1 = Chain_A**pull_rate1 = 0.01 ; 0.01 nm
per ps = 10 nm per ns
**pull_k1 = 1000 ; kJ mol^-1 nm^-2*
Pull_rate1 = velocity variable for CVP
Pull_k1 = is this option is for constant force pulling OR THIS IS SPRING
CONSTANT FOR THE VIRTUAL SPRING???
because i am trying to follow Justin's umbrella sampling tutorial and when
i remove this PULL_K1 option...then the COM Pull Energy ... does not change
and the ligand never get pulled away.??
Per the manual:
"The force constant. For umbrella pulling this is the harmonic force constant in
[kJ mol-1 nm-2]. For constant force pulling this is the force constant of the
linear potential, and thus minus (!) the constant force in [kJ mol-1 nm-1]."
If you do not specify it in the .mdp file, its default value (again, in the
manual) is zero, so it will of course do nothing.
-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 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
