On 7/17/13 8:09 AM, pooja_gu...@nccs.res.in wrote:
okk
This may be very basic question.
I took a natural pdb and unfold with SAMD. I ran simulation for 10ns. I
picked up one unfolded structure from the trj and solvated with water. I
ran em for full system. now i am calculating the entropy. I afraid if i
missed something.
Are you running g_covar on the original 10 ns trajectory, or on a single
energy-minimized structure? That latter would not make sense.
I am doing this first time.
There is a large body of literature on configurational entropy related to the
quasiharmonic approximation. I would suggest you look into its underlying
theory and how others apply it to biomolecular simulations.
-Justin
On 7/17/13 7:56 AM, pooja_gu...@nccs.res.in wrote:
I used system (0) for g-covar.
Most likely, g_anaeig is running out of memory. Try using some subset of
the
system, like the protein only or its backbone.
-Justin
On 7/17/13 7:42 AM, pooja_gu...@nccs.res.in wrote:
thanks for reply
i am using Gromacs 4.5.5 version
command
g_anaeig -v *.trr -entropy -s *.tpr -extr -f *.pdb -rmsf -3d -comp
What was the g_covar command used to generate the eigenvector .trr
file?
What
group did you choose for analysis during g_covar?
-Justin
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Justin A. Lemkul, Ph.D.
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==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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