[gmx-users] define = -DPOSRES_B??
jalemkul at vt.edu
Mon Jun 4 13:58:42 CEST 2018
On 6/3/18 7:55 AM, m g wrote:
> Dear Justin,I fellow your tutorial " Umbrella Sampling", I want to pull a protein across the membrane but I don't know how set the "define" section.
What you need to do does not require any special restraints. See
previous posts on this topic. The restraints used in the tutorial are
unique to that type of system; please read the article linked from the
tutorial and references therein to understand why we did what we did.
> This is my pull code:pull = yespull_ngroups = 2pull_ncoords = 1pull_group1_name = DPPCpull_group2_name = Proteinpull_coord1_type = umbrella ; harmonic biasing forcepull_coord1_geometry = direction ; simple distance increasepull_coord1_groups = 1 2pull-coord1-vec = 0 0 1pull_coord1_rate = 0.005 ; 0.005 nm per ps = 5 nm per nspull_coord1_k = 700 ; kJ mol^-1 nm^-2pull_coord1_start = yes ; define initial COM distance > 0
> would you please help me?best regards, Ganj
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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