[gmx-users] Umbrella Sampling tutorial

[Dr. Vitaly Chaban]

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 <jalemkul at 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
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