[gmx-users] constraint pulling

[Justin Lemkul]

On 3/19/14, 5:07 AM, leila karami wrote:
> Dear Justin
>
> My system contains lipid + drug + water molecules.
>
> At first, I put drug molecule in middle of bilayer.
>
> Based on your tutorial, after minimization and equilibration, I generated
> configurations. After using distance.pl script, summary_distances.dat file
> is irregular such that no increasing trend is not seen in the distances. Some
> times distance increased and some time decreased.
>
> Is there problem in generating configuration step?
>
>
>
>
>
>
>
> pull code part of mdp file is as follows:
>
> pull = constraint
> pull_geometry = distance
> pull_constr_tol = 1e-6
> pull_dim = N N Y
> pull_ngroups    = 1
> pull_group0     = CHOL_DOPC
> pull_group1     = drug
> pull_vec1 = 0 0 1
> pull_rate1= 0
> pull-start = yes
>
> How to resolve this issue?
>

If you're using these settings to generate configurations, you need a non-zero 
value of pull_rate1.

-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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