The dynamic works, but I still have the same problems with minimization...
"Justin A. Lemkul" <jalem...@vt.edu> ha scritto:
vferra...@units.it wrote:
Ok and which definition have you used? the previous one with 5 atom
for molecule?
Yes.
-Justin
"Justin A. Lemkul" <jalem...@vt.edu> ha scritto:
vferra...@units.it wrote:
Just the last thing... can you copy your mdp file? I think I'm
having some problems also with that... Thanks.
For EM, I used the .mdp file you posted in your first message and
added the line "continuation = yes." For MD, I changed nstlist
from 100 to 5.
-Justin
Valerio
"Justin A. Lemkul" <jalem...@vt.edu> ha scritto:
Justin A. Lemkul wrote:
<snip>
I've obtained a stable trajectory for a single CHCL3 molecule.
By setting "continuation = no" (so that constraints are not
solved before step 0) in the em.mdp file, and then reducing
nstlist to 5 in md.mdp, I
Ack, this should be "continuation = yes." Sorry for the
confusion. I will copy from my .mdp file...I will copy from my
.mdp file... :)
-Justin
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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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========================================
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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