mohsen ramezanpour wrote:
Dear Dr.Justin
Thank you for your reply
My is Protein-ligand,It is have the same conditions as tutorial.I did
pull ligand in the z direction.
Actualy I found your note about gen_vel ,but I didn't any about
Continuation!
Not that specific keyword, no, but I do address the general principle about
continuing these simulations via this very discussion about gen_vel.
You are right,But there is another problem:
You have not used any -t option in grompp command (doing
umbrella step).
Correct. See the discussion on gen_vel that I referenced earlier.
Since we have set Continuation=yes;
Can grompp realize from which .cpt (npt.cpt ) it must use ?
grompp does not make any choice about what it should use. It takes whatever
input you give it and assembles a run input file. If you're following my
procedure (which may or may not necessarily be applicable in all cases), then
there will NOT be a suitable .cpt file for each starting configuration. These
configurations were generated using SMD, and .cpt files are not written and
saved at every frame so you have a corresponding one later.
And my last question:
Do I need to any .cpt file ? (Because I have set Continuation=yes)
Checkpointing and continuation are related, but not identical. The
"continuation" keyword deals with whether or not constraints are solved before
the first integration step. It otherwise has nothing to do with the
thermodynamic state of the system, which is contained in the .cpt file.
For your system, as I state in the tutorial, you may want to set "gen_vel = yes"
in each window (since there is no prior equilibration, which may be a problem
for some systems, but not the tutorial example). This would eliminate the need
for a .cpt file.
-Justin
Thanks in advance
On Mon, May 2, 2011 at 3:27 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
mohsen ramezanpour wrote:
Dear Dr.Justin
Regarding Umbrella Sampling tutorial:
The CONTINUATION option in md_umbrella.mdp is YES,
and you have noticed : From NPT
I can't understand it's reason correctly!
This is a meaningless comment. It was left there from copying and
pasting files before modifying them. The important part is that
"continuation = yes" be set to correctly solve the constraints.
we run a NPT and then Pulling, then extracted some
configurations from pull.trr file.
I think we must continue from pull.cpt not NPT.cpt
I mean :
grompp -f md_umbrella.mdp ............................. -t
pull.cpt is more correct than
grompp -f md_umbrella.mdp .............................. -t
NPT.cpt
am I right?
In the case of the tutorial, no. There is not a corresponding .cpt
file for each configuration generated. If you were to somehow apply
the same .cpt file for each configuration, almost certainly some of
the windows would blow up because the initial velocities would cause
nasty collisions. Note that I discuss the continuation issue,
proper settings for gen_vel, etc. in the tutorial, step six.
-Justin
Thanks in advance for your reply
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://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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