[gmx-users] Gromacs 5 umbrella sampling

[Justin Lemkul]

On 4/3/14, 4:06 PM, Andres Ortega wrote:
> Dear Gromacs User, i am trying to use US, with gromacs 5,
> I was trying to do a position umbrella sampling so this is my pull code,
> but i get an error about the pull-coord1-groups,
> there's no nome group0 and group1 , so how should i define this,

When reporting an error, please always copy and paste the full error message 
from the terminal.  It's hard to diagnose what's going on without all the 
information.

> or in pull-coord1-groups are the numbers of the groups in the index file?
> in the manual said that the first one should be 0 and the second one?
>

The manual doesn't say that.  It says the value "can be 0," which is actually 
not what one would normally do.  The default group 0 in Gromacs is "System" and 
thus you are relying on an absolute reference.

-Justin

> Could you explain to me this? thanks
>
> ; Pull code
> pull            = umbrella
> pull_geometry   = direction  ;
> pull_coord1_vec       = 0.0 0.0 1.0 ;
> pull_start      = yes       ; define initial COM distance > 0
> pull_coord1_init      = 0.0
> pull_ngroups    = 1
> pull_group0_name     = protein2pull
> pull_group1_name    = DOX
> pull_coord1_rate      = 0.0      ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k         = 800     ; kJ mol^-1 nm^-2
>
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/Gromacs-5-umbrella-sampling-tp5015616.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

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

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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