[gmx-users] umbrella sampling using pull codes

[Justin Lemkul]

On 9/12/13 9:55 AM, mjyang wrote:
> Dear GMX users,
>
>     I'd like to perform the umbrella sampling using the pull codes in gromacs. The reaction coordinate is defined as the distance between the center of mass (DCOM) of two domains in a protein. The following script is used:
> ------------------- only for pull section
> ; Pull code
> pull            = umbrella
> pull_geometry   = distance
> pull_dim        = N N Y
> pull_start      = no
> pull_ngroups    = 1
> pull_group0     = NN1 ; contained in index file
> pull_group1     = NN2 ; contained in index file
> pull_init1      = 2.5
> pull_rate1      = 0.0
> pull_k1         = 20000      ; kJ mol^-1 nm^-2
> pull_nstxout    = 5000      ; every 2 ps
> pull_nstfout    = 5000      ; every 2 ps
> -----------------
>
> I have two questions about the output of gromacs:
> 1. How is the energy term "COM Pull En." in *.log file calculated? Is it computed as 1/2*kf*(DCOM_t -  pull_init1)^2 at time t?

Sounds right.  It's something that's very easy to calculate yourself from a 
given trajectory frame to confirm.

> 2. Where is the output information for the evolution of DCOM? Is it in the file pullx.xvg?
>

Yes.

-Justin

-- 
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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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