[gmx-users] Gentle heating with implicit solvent

[Justin Lemkul]

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" <gianluca at 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 gianluca at 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 gianluca at 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.
> -----------------------------------------------------

-- 
==================================================

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================