[gmx-users] GMX 2018 and 'distance' pull

[Justin Lemkul]

On 3/13/18 7:16 AM, Justin Lemkul wrote:
>
>
> On 3/13/18 2:38 AM, Alex wrote:
>> Hi all,
>>
>> There seems to be a problem with the new pull code when it comes to 
>> using it for umbrella sampling with 'distance' directive for WHAM 
>> (the original thread is my earlier exchange with Justin in 
>> '[gmx-users] seeming paradox with gmx wham'). In order to subdue 
>> unknown statement errors, the code was modified to:
>>
>> pull                 = yes
>> pull-coord1-type     = umbrella
>> pull_ngroups            = 2
>> pull_ncoords            = 1
>> pull_group1_name        = K
>> pull_group2_name        = CNT
>> pull_coord1_geometry    = distance
>> pull_coord1_groups      = 1 2
>> pull-coord1-dim         = Y Y Y
>> pull_coord1_rate        = 0.0
>> pull_coord1_k           = 1000
>> pull_coord1_start       = yes
>>
>> But it is a mess anyway. The box is 5.7 nm tall (6 nm by 5.5 nm wide) 
>> and the membrane's COM is definitely close to the geometric center of 
>> the box and it is definitely not moving beyond a few angstroms from 
>> thermal fluctuations (the membrane is very strongly restrained at its 
>> perimeter). The initial coordinate configurations for the other group 
>> (an ion) are a sweep of heights between -1.5 nm and 1.5 nm right 
>> relative to the membrane's COM along the height -- initial x and y 
>> are those of the membrane's COM -- see my very angry drawing here: 
>> https://www.dropbox.com/s/bwugqp5v9qt7iaq/pull.jpg?dl=0   :) The 
>> distance simply cannot exceed 1.5 nm with spherical symmetry, it just 
>> can't. And yet, i get errors like
>>
>> "Distance between pull groups 1 and 2 (3.035939 nm) is larger than 
>> 0.49 times the box size (2.728418)." -- this is from grompp
>>
>> Sometimes grompp is actually satisfied, but then mdrun throws this 
>> after a few thousand steps:
>>
>> "Program:     gmx mdrun, version 2018
>> Source file: src/gromacs/pulling/pull.cpp (line 707)
>> MPI rank:    0 (out of 2)
>>
>> Fatal error:
>> Distance between pull groups 1 and 2 (2.732163 nm) is larger than 
>> 0.49 times
>> the box size (2.728418)."
>>
>> This does not seem possible, because at this point the ion is 
>> radially restrained (1000 kJ/mol/nm2). This was /never/ an issue with 
>> 5.0.4 with a considerably smaller box (4 nm) -- the entire mdp file 
>> is a copy of what worked in 5.0.4, except the pull code is as above. 
>> Do I just continue increasing the box size?
>>
>
> You may have a situation that requires manual assignment of 
> pull_group1_pbcatom1, as the automatic choice of 

Sorry, that should be pull_group1_pbcatom. Must remind myself not to 
email before coffee...

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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