Re: [AMBER] MD simulation parameters: urgent please

From: Mary Varughese <>
Date: Tue, 2 Jul 2013 07:31:49 +0530

The system has some 6952 water molecules (explicit simulation)
can i go with gamma_ln=1?
somehow i missed taup=2.0 in my input of the simulation i had run.
Is taup=2.0 essential?
now i will use ig=-1 also.
 i am used to center and image commands in ptraj for reimaging . should i
switch to autoimage of cpptraj?
could u please explain about wrapping artifacts. how can i check it, just

Also sir, on doing rms first mass of a dna ligand system;
rms first mass :1-24.P,O3',O5',C3',C4',C5' time 1.0
does this command take care of my ligand :25 also.
or should i use
rms first mass :1-24.P,O3',O5',C3',C4',C5' :25 time 1.0
but this command output says nothing about :25
how can i now ligand is also rms fitted?

On Tue, Jul 2, 2013 at 7:08 AM, David A Case <>wrote:

> On Mon, Jul 01, 2013, Mary Varughese wrote:
> >
> > in the production dynamics(in NPT):
> > when ntb=2, ntp=1, pres0=1.0, ntt=3
> >
> > 1: what should be the appropriate value of gamma_ln ? (i have used 1 )
> > does increasing value to 5.0 has any advantage
> I doubt that you could see any difference between 1 and 5.
> > 2: also what is the significance of taup=2.0 ; how does it affect the
> > dynamics
> The affects the speed at which the volume of the system responds to
> pressure
> fluctuations, and hence to the magnitude of the fluctuations themselves.
> If your system is too small (doesn't have enough water molecules) the
> value
> of this variable might cause a noticeable difference, although I have not
> personally seen such a case.
> > 3: also should i essentiallly include ig=-1 as it says in amber DNA
> > tutorials in the case of ntt=3.
> Yes: this is essential.
> > 4: Also i hope adding these values doesnt affect mmpbsa calculations.
> Not setting ig=-1 could lead to very bad results. Minor variations in
> gamma_ln or taup are unlikely to have measurable effets.
> >
> > 5: Also sir does iwrap=1 has any influence on mmpbsa calculations?
> It can. The safest course of action is to use the "autoimage" command in
> cpptraj before handing things off to mm-pbsa. Also, be sure to visualize
> your trajectory (after autoimage) to make sure there are no wrapping
> artifacts.
> ...dac
> p.s.: be sure to study reviews of mm-pbsa calculations, and look for
> papers that report calculations similar to the ones you are planning. In
> my opinion, a careful study of what happens during your simulation is a
> lot more likely to lead to new insights than are the energies that come
> out of the mmpbsa analysis.
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Received on Mon Jul 01 2013 - 19:30:03 PDT
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