[gmx-users] Gromacs 5 umbrella sampling

[Justin Lemkul]

On 4/4/14, 8:33 AM, Andres Ortega Guerrero wrote:
>
>
>
> I'm sorry Justin, My mistake,
>
> when i use this pull code, using grompp, with this pull code
>
> ; Pull code
> pull            = umbrella
> pull_geometry   = direction  ;
> ;pull_vec1       = 0.0 0.0 1.0 ;
> pull_coord1_vec       = 0.0 0.0 1.0 ;
> ;pull_dim        = N N Y
> pull_start      = yes       ; define initial COM distance > 0
> pull_coord1_init      = 0.0
> pull_ngroups    = 1
> pull-coord1-groups = 0 1
> pull_group0_name    = protein2pull
> pull_group1_name    = DOX
> ;pull-r1         = 1.0
> ;pull-r0         = 1.0
> pull_coord1_rate      = 0.0      ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k         = 800     ; kJ mol^-1 nm^-2
> ;pull_k1         = 800     ; kJ mol^-1 nm^-2
>
> this is the error
>
> Pull group  natoms  pbc atom  distance at start     reference at t=0
>         0         0         0
>         1        68     57366
> -------------------------------------------------------
> Program grompp, VERSION 5.0-beta2
> Source code file: /home/bionano/Desktop/gromacs-5.0-beta2/src/gromacs/pulling/pull.c, line: 337
>
> Fatal error:
> Distance between pull groups 0 and 1 (8.777763 nm) is larger than 0.49 times the box size (5.774220)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> but the problem is that hi is assuming 0 as the system, but i want to use as in gromacs 4.6.5 group0 as protein2pull, define in my index file,
> which is in an appropriate distance, and if i use the index number from the index file in the coord1-group. it appears that the must be between 0-3
> The initial configuration where made in gromacs 4.6.5 and the index file too
>

Caveat: I've never used 5.0 for pulling, so I'm going only based on what I read 
in the manual here.

It seems like the indices specified in pull-coord1-groups need to match whatever 
is specified in pull_group[01]_name.  So if your group0 is "protein2pull," then 
the matching index shouldn't be zero, which it appears grompp is reading as the 
entire system.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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