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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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