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

[Kalyanashis]

Thank you Justin.. I have done the calculation with "pull_vec1= 0.0 0.0 1 "
option but do not get the expected result. Actually, I want to push the
drug molecule to its initial position i.e. after pulling it has come out
from the active site of the enzyme now I want to push it to the active
site. Please suggest me the probable solution to solve this problem.
Thanks in advance,
Kalyan.


On Thu, Apr 24, 2014 at 5:47 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5016040h27 at n6.nabble.com> wrote:

>
>
> 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
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-- 
Kalyanashis Jana
email: kalyan.chem.in at gmail.com


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