Amir Marcovitz wrote:
Hi,
my system is constructed of 2 parallel plates in a box with solvent.
each plate is made of 36 atoms which are positively charged on one of
them (SRP) and negatively charged on the other plate (SRN).
i want to perform a simulation with umbrella sampling between the 2 so i
defined the pulling section parameters in the .mdp parameter file as
following:
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = umbrella
; Pull geometry: distance, direction, cylinder or position
pull_geometry = distance
; Select components for the pull vector. default: Y Y Y
pull_dim = Y Y Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1 = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0 = 1.5
pull_constr_tol = 1e-06
pull_start = no
pull_nstxout = 10
pull_nstfout = 1
; Number of pull groups
pull_ngroups = 2
; Group name, weight (default all 1), vector, init, rate (nm/ps),
kJ/(mol*nm^2)
pull_group0 = SRP
pull_weights0 = 1
pull_pbcatom0 = 0
pull_group1 = SRN
pull_weights1 = 1
pull_pbcatom1 = 0
pull_vec1 = 0.0 1.0 0.0
pull_init1 = 1.5
pull_rate1 = 0
pull_k1 = 1
pull_kB1 = 0
when proccesing the file with grompp i get the following error:
*Fatal error:
Number of weights (1) for pull group 0 'SRP' does not match the number
of atoms (36)*
is someone recognizing my mistake?
Please refer to the manual (manual.gromacs.org is quite handy), you will find:
"Optional relative weights which are multiplied with the masses of the atoms to
give the total weight for the COM. The number should be 0, meaning all 1, or the
number of atoms in the pull group."
I also think your value for pull_ngroup is wrong. It appears you are pulling
SRN with respect to SRP, so you only have one pull group, not two.
-Justin
does someone has an experience with umbrella sampling in GROMACS?
thanks'
amir
*
*
--
========================================
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/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/mailing_lists/users.php
