[gmx-users] Com pulling in reverse Z direction in SMD simulation..

[Justin Lemkul]

On 4/24/14, 5:21 AM, Kalyanashis wrote:
> Dear all,
>    I am doing SMD simulation of a enzyme system and I have given the pull
> option in Z direction. The com pulling options are given below,
> ;COM pulling
> pull                     = umbrella
> pull_geometry            = distance
> pull_dim                 = N N Y
> pull_r1                  = 1
> pull_r0                  = 1
> ;pull_constr_tot          = 1e-6
> pull_start               = yes
> pull_nstxout             = 10
> pull_nstfout             = 1
> pull_ngroups             = 1
> ;name of reference group
> pull_group0              = Protein
> ;pull_weights             = 0
> ;name of pull group
> pull_group1              = UNK
> ;pull_weights             = 0
> pull_vec1                = 0.0 0.0 -1
> ;ref. distance at t=0
> ;pull_init1               = -2.4477384   -1.0229216   -1.5900776
> ;rate of change of ref. gr. [nm/ps]
> pull_rate1               = 0.0005
> ;force constant [KJ mol^-1 nm^-2]
> pull_k1                  = 1586.747
> ;pull_kB1                =
>
> Please kindly tell me, how can I do the same calculation in reverse Z
> direction??

Change the sign of the pulling vector.

-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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