Amit Choubey wrote:
Hi all,
I am trying to do pulling simulation. Following are the pull parameters
pull = umbrella
pull_geometry = direction
pull_vec1 = 0 0 1
pull_group1 = RNA
pull_rate1 = 0.01
pull_k1 = 1000
pull_start = yes
Everything works fine until the pull group COM reaches half the box
length. The COM position changes by the box length and that causes huge
force on the group. What should i do to fix this ? Also i am using NPT
coupling.
You have to use a sufficiently large box, otherwise the periodic distance
becomes the reference distance when this happens. This has been discussed
numerous times on the list (hint: there is an archive for a reason!) and in the
tutorial linked here:
http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling
-Justin
Amit
--
========================================
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
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