On 11/4/13 2:25 PM, Gianluca Interlandi wrote:
Dear Mark,
Sorry for replying to an older thread. We are trying to perform implicit solvent
simulations of protein G with CHARMM27 in gromacs. We are trying to trouble
shoot why the protein unfolds after already 2 ns of dynamics. We use simulated
annealing for the heating with 1 fs time step. The thermostat is v_rescale and
OBC is the GBSA algorithm. Do you have any suggestions what we could improve?
You mention using a sub-fs time step for the equilibration. Do you still use
LINCS? Do you use simulated annealing to heat up the system or do you just apply
position restraints to the heavy atoms?
A complete .mdp file would be helpful. Are you using finite cutoffs?
-Justin
Thanks,
Gianluca
On Wed, 28 Aug 2013, Mark Abraham wrote:
It can be. Lack of explicit degrees of freedom of solvent can make
achieving equipartition tricky. With CHARMM27 and virtual sites in implicit
solvent, I have sometimes found it necessary to use a sub-femtosecond time
step at the start of equilibration, even where there were no atomic
clashes. Maybe the system was just unlucky with generating velocities,
though :-)
Mark
On Aug 28, 2013 7:16 AM, "Gianluca Interlandi" <gianl...@u.washington.edu>
wrote:
How important is it to do gentle heating (using simulated annealing) with
GBSA? Often with explicit water it is enough to perform some equilibration
with positional restraints. Would it be enough to do the same with implicit
solvent?
Thanks,
Gianluca
------------------------------**-----------------------
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.**washington.edu/<http://artemide.bioeng.washington.edu/>
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
------------------------------**-----------------------
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-----------------------------------------------------
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------
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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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