[gmx-users] Umbrella Sampling tutorial

[shahab shariati]

Dear Justin

When I placed drug within the lipid bilayer, after Generating Configurations
step, I obtained 501 gro files. When I used distance.pl script for these
gro files, my summary_distances.dat file is as follows:

0    0.2756352
1    0.2535359
2    0.2447009
3    0.3004653
4    0.2936225
5    0.1910549
6    0.2493761
7    0.2033079
8    0.1769952
9    0.2731782
10    0.2927040
11    0.3717106
12    0.3232497
.
.
.
.
485    0.7589852
486    0.6876000
487    0.6966222
488    0.7487700
489    0.7043532
490    0.6424745
491    0.7194880
492    0.6209456
493    0.6327312
494    0.6861565
495    0.5513341
496    0.6917742
497    0.7074009
498    0.7403648
499    0.6833771
500    0.7035147

As can be seen the range of distance is 0.27-0.7, while the dimensions of
box is  5.92819   6.43131   7.75764.

My supposition was that the range of distance should be 0-3.9 (7.75764/2).

You are right. The settings depend on where I place everything.
This is my first experience in com pulling. Please guide me to use
appropriate Pull code parameters in my case (drug molecules within the
lipid bilayer).

I used following Pull code parameters:

; Pull code
pull            = umbrella
pull_geometry   = position  ; simple distance increase
pull_dim        = N N Y
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = CHOL_DOPC
pull_group1     = drg
pull_rate1      = 0.001      ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 100      ; kJ mol^-1 nm^-2
pull_init1      = 0
pull_vec1       = 0 0 1

Except Pull code parameters, what things are important?

Best wishes.