Hi,
Unfortunately, just because a system looks like its in a reasonable
conformation doesn't always mean that it is, particularly when
explicit solvent is involved. You probably need a better minimization
procedure. In particular you may need to apply positional restraints
to heavy atoms during the initial relaxation of solvent. You will also
at some point need to run using constant pressure (NTP) to equilibrate
your solvent density.
-Dan
PS - In my opinion it's generally not useful to heat the system up
from a low temperature for the purposes of equilibration; it's far
better to just go with randomized velocities at your temperature of
interest (i.e. tempi = temp0).
On Sun, Oct 19, 2014 at 12:49 PM, jinfeng liu <jinfengliu1119.gmail.com> wrote:
> Dear Amber users,
>
> I want to run constant pH MD simulations for one protein, which contains a
> ligand, in explicit water with Amber14. First, I minimized the system with
> a constraint on the protein backbone atoms, and there was nothing wrong in
> the minimization. Then I wanted to heat the system from 0 K to 300 K. But
> the system always collapsed, and the heating procedure died. I guess it is
> the ligand's problem, because when I heated the system without the ligand,
> it could safely heat to 300 K. I calculated the atomic charges of the
> ligand in AM1-BCC charge model with antechamber, and I think there was
> nothing wrong in this process. And I have checked the initial structure of
> ligand, it looked reasonable. Can anyone tell me why ? The following is the
> heating input file:
>
> Explicit solvent initial heating mdin
> &cntrl
> imin=0, irest=0, ntx=1,
> ntpr=1000, ntwx=1000, nstlim=200000,
> dt=0.002, ntt=3, gamma_ln=5.0, ig=-1,
> ntc=2, ntf=2, cut=12, ntb=1,
> iwrap=1, ioutfm=1, nmropt=1,
> /
> &wt
> TYPE='TEMP0', ISTEP1=0, ISTEP2=150000,
> VALUE1=10.0, VALUE2=300.0,
> /
> &wt TYPE='END' /
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sun Oct 19 2014 - 12:30:02 PDT
