[gmx-users] pH and Temperature

[Justin Lemkul]

On 1/13/14, 4:17 PM, Mostafa Javaheri wrote:
> ​Dear Justin
>
> I want to
> simulate a protein in human’s body temperature (37° Celsius,
> 98.6° Fahrenheit),
> Is
>   this OK to set ref-t: 310 in nvt.mdp file or I have to start from lower
>   temperature
> e.g. 300, 200, 100 then increasing it step by step till reaching the
> desired
> temperature? Will the simulation be OK if I start from 310 K? Many

I rarely use annealing.  Occasionally it is useful, but for a protein in water I 
find no compelling reason.

> researchers prefer 300 k, is this the optimum temperature for all
> GROMACS simulation?

No, you need to model whatever is appropriate for the system at hand. 
Experimental and biological conditions vary.

>
> What is the default pH value for mdrun and could I change it?
>

There is no default pH value.  mdrun does what you tell it, which is to apply 
the static topology that you assign when running pdb2gmx.  Normally, pdb2gmx 
assigns charged states to all titratable residues, except histidine, which has 
its protonation state assigned based on hydrogen bonding geometry.  If you want 
to model a different protonation state (there is no such thing as pH in a 
traditional MD simulation, though more advanced methods exist for proton 
exchange and/or dynamic protonation states) then you need to calculate pKa 
values for all titratable residues and make the appropriate selections during 
pdb2gmx for the charge state you want.

-Justin

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

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

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