parto haghighi wrote:
Dear Justin
thank you for your response
here is my umbrella part of mdp file:
; Pull code
pull = umbrella
pull_geometry = position ; simple distance increase
pull_dim = N N Y
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = DRUG
pull_group1 = LIPID
pull_rate1 = 0.1 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000 ; kJ mol^-1 nm^-2
pull_init1 = 0 0 0
pull_vec1 = 0 0 1
I want to pull drug to lipid bilayer.when i run with this mdp i have
this error: pull_vec1 can not be zero when pull position and non-zero
pull_init1
Could you please help me?!
Please copy and paste the full error message from the terminal. I cannot find
that error in the source, though I find two similar ones, both indicating
something slightly different.
In any case, you've got several parameters that need changing for this to work.
First, with the "position" geometry, you do not need pull_dim, as the pulling
direction is read from pull_vec1. Second, in order to pull the drug closer to
the membrane, you need a negative pull rate. As it stands, you're telling mdrun
to move the drug such that it causes a positive change in COM distance.
Otherwise, use the positive pull_rate1 and a negative vector along which to do
the pulling (pull_vec1); both approaches should achieve the same end.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
