# Re: [gmx-users] Umbrella Sampling tutorial

```The output you got indicates that the pulled group came to the
location where it is expected by gromacs to be.```
```
The input looks correct, but gromacs' pull code is with surprise
inside. I would try to pull in opposite direction, i.e. pull_vec1 = -0
0 1. Turning off barostat during pulling also saves nerves.

It must be possible to pull through the whole box, not up to the
middle of Z side.

Dr. Vitaly V. Chaban

On Sun, Dec 1, 2013 at 5:07 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 12/1/13 10:38 AM, shahab shariati wrote:
>>
>> 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?
>>
>
> I have never attempted such a pulling procedure.  Hopefully someone else
> will comment on their experiences.  Do not try to hack the tutorial into
> working for your system; the approaches will be quite different.  The manual
> explains the logic behind the different geometries; you may have to
> experiment a bit to get things to work.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
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