Hello all,
Thank-you for the reply Jason. I am interested in the non-bonded only
dynamics so I think ntf = 7 is the right choice. Also I have changed to
doing NVT heating over 20 ps which maintains the atoms in their current
position as you said. However at the end of this process the water density
is too low (around 0.63 g/cc) so I think that means I should do an NPT
equilibration to bring the water density to its equilibrium value, but this
again produces the drifting issue.
All the .in, inpcrd, prmtop and .out (equil-file.out shows the water
density being equilibrated):
https://www.dropbox.com/sh/d7nrfga8nwr112u/AACNmY-LQNd04_SEcOSUSfrAa?dl=0
Here are the steps I take: 1) Minimize, 2) Heat at NVT for 20 ps, 3)
Equilibrate at NPT
Here are the commands I used:
sander -O -i min.in -o min-file.out -p file.prmtop -c file.inpcrd \
-r min-file.rst -inf min-file.mdinfo -ref file.inpcrd
sander -O -i heat.in -o heat-file.out -p file.prmtop -c min-file.rst -r
heat-file.rst \
-x heat-file.mdcrd -inf heat-file.mdinfo -ref file.inpcrd
sander -O -i e <
http://heat.in/>quil.in -o equil-file.out -p file.prmtop -c
heat-file.rst -r equil-file.rst \
-x equil-file.mdcrd -inf equil-file.mdinfo -ref file.inpcrd
Is there a way I can equilibrate the water density while keeping the
restrained molecules in the same position?
Thank-you,
Sanmeet
On Fri, Mar 20, 2015 at 8:22 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, Mar 19, 2015 at 6:32 PM, Sanmeet Chahal <schah063.uottawa.ca>
> wrote:
>
> > Hello all,
> >
> > I am trying to run a simulation with two of the molecules being
> restrained
> > to their original positions. However after I visualize the trajectory
> with
> > VMD, the restrained molecules show a drift from their current position
> over
> > time.
> >
> > The prmtop, inpcrd, and in files can be found here:
> >
> https://www.dropbox.com/sh/ecng1mjobglgy6i/AAAIydLyGWe2O-e-2PnS5M-sa?dl=0
> >
> > My procedure is the following:
> > 1) minimize, 2) heat at NPT conditions
> >
> > Here are the commands I used :
> >
> > sander -O -i min.in -o min-file.out -p file.prmtop -c file.inpcrd \
> > -r min-file.rst -inf min-file.mdinfo -ref file.inpcrd
> >
> > sander -O -i heat.in -o heat-file.out -p file.prmtop -c min-file.rst -r
> > heat-file.rst \
> > -x heat-file.mdcrd -inf heat-file.mdinfo -ref
> file.inpcrd
> >
> > I have found that someone was having similar issues before:
> > http://archive.ambermd.org/201302/0115.html
>
>
> I see a number of unrelated issues with your input file:
>
> You set ntc=2 to turn on shake, but then set ntf=7 to prevent any bond,
> angle, or dihedral forces from being calculated (!!) This will most likely
> render your simulation results meaningless. So you should set ntf=2 (with
> ntc=2) unless you *know* what you're doing and wanted to see nonbonded-only
> dynamics for whatever reason.
>
> Also, you are running constant pressure simulations when your temperature
> is initially 0 K. This can cause weird behavior. My suggestion is to heat
> up at constant volume rather quickly (over 10 to 100 ps), then switch to
> constant pressure in order to equilibrate density.
>
> Finally, your restraint weight is *incredibly* large. I would suggest a
> value one to two orders of magnitude smaller. (A value of 20 will
> definitely keep your first two residues fixed in place, without introducing
> overly high vibrational frequencies).
>
> Also, nsnb is really no longer useful. It's ignored for MD, and
> generally unnecessary for minimizations. I would suggest removing
> variables from the input file that you're not using, or that you are just
> setting to their default value. Same goes for ew_type -- there is *very*
> rarely an instance where you would want to do an Ewald calculation
> (ew_type=1) rather than a PME calculation (ew_type=0, default).
>
> I attempted to use the suggestion by setting nscm to be larger than nstlim
> > but this problem still persists.
> >
>
> One thing that I know happens when you use restraints with constant
> pressure simulations is that the reference coordinates are "scaled" with
> the regular coordinates when the box grows or shrinks (in order to
> accommodate the effect of the external pressure). This is a *good* thing,
> but as the box "breathes" it can give the appearance of restrained atoms
> 'drifting' during the simulation.
>
> You can see if this is the actual cause by running a NVT simulation during
> your heating stage instead and making sure that the effect goes away.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 20 2015 - 07:30:03 PDT
