[gmx-users] Gentle heating with implicit solvent

[Gianluca Interlandi]

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?

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.
-----------------------------------------------------