[gmx-users] pH and Temperature
jalemkul at vt.edu
Mon Jan 13 23:49:56 CET 2014
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),
> this OK to set ref-t: 310 in nvt.mdp file or I have to start from lower
> e.g. 300, 200, 100 then increasing it step by step till reaching the
> 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 A. Lemkul, Ph.D.
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
More information about the gromacs.org_gmx-users