[gmx-users] umbrella sampling using pull codes

[mjyang]

Dear Justin,

Thanks for your reply. I checked the content in pullx.xvg file as follows:
--------------------------------------------------------
# GRowing Old MAkes el Chrono Sweat
#
@    title "Pull COM"
@    xaxis  label "Time (ps)"
@    yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 Z"
@ s1 legend "1 dZ"
0.0000  6.50285 -0.206062
10.0000 7.66133 -2.6497
20.0000 7.65877 -2.65375
30.0000 7.65128 -2.6575
40.0000 7.64102 -2.66939
--------------------------------------------------------------

The numbers in 1st column is time. What is the meaning of the numbers in the 2nd and 3rd columns? 

Many thanks.

Mingjun

________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin Lemkul [jalemkul at vt.edu]
Sent: Thursday, September 12, 2013 10:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling using pull codes

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

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

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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