[gmx-users] density profile

[Elisabeth]

Thanks Justin for your reply. To avoid compressing down the cell I thought
using semiisotropic option with 0 compressibility in Z would be
appropriate.

Here are the steps:

1- First I did a 10 ns NPT to equilibrate the box and used the last frame
gro and cpt file as input for the next step
2- I extended the box in Z to more than twice the initial box size and
issued the following:

grompp -f md.mdp -c extendedZ.gro -t .cpt -p .top -o extendedZ.tpr
mpirun -np 4 mdrun_mpi -deffnm .extendedZ -s -o -c -g -e -x -v

My questions are:

1) Can I get the proper solvent-air interface to obtain density profile by
extending the Z direction (last line of the gro file obtained from NPT at
each pressure)? Is that what yo mean by " then build a new unit cell and
run under NVT" ?
2) Is the semi isotropic option with 0 compressibility in Z is appropriate
to keep the pressure fixed? (as shown below in mdp settings)?
3) If the answer to q 2 is negative, whats is appropriate way to shift from
NPt to NVT run. Do I have to use the equilibrated density from NPT runs and
edit the last line of gro from -c flag of NPT.gro to obtain the correct
density? The reason I am asking is that since P fluctuations are huge I am
not sure if the the density of box from last frame of -c NPT.gro output is
the correct density...

Please advise on the above queries..Thanks a lot





Below is the md.mdp contents:

pbc                 =  xyz


integrator          =  md

dt                  =  0.001

nsteps              =  20000000

nstcomm             =  100



;           Output control

nstenergy           =  100

nstxout             =  100;1

 nstvout             =  0

nstfout             =  0

nstlog              =  1000

nstxtcout           =  1000

;           Neighbor searching

nstlist             =  10

ns_type             =  grid

;           Electrostatics/VdW

coulombtype         =  Shift

vdw-type            =  Shift

rcoulomb-switch     =  1

rvdw-switch         =  1 ;0.9

;           Cut-offs

rlist               =  1.35

rcoulomb            =  1.1   ;1.1

rvdw                =  1.1


Tcoupl              =  v-rescale

tc-grps             =  System

tau_t               =  0.1

ref_t               =  425

*   *

*Pcoupl              =  berendsen*

*Pcoupltype          =  semiisotropic                 *

*tau_p               =  1      0.5                *

*compressibility     =  3.5e-5  0*

*ref_p               =  50   ** *



gen_vel             =  no

gen_temp            =  500.0

gen_seed            =  173529



constraints         = none

constraint-algorithm = lincs


On 31 March 2013 12:47, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/31/13 12:27 PM, Elisabeth wrote:
>
>> Thank Justin. I am interested in the density profile at the solvent-air
>> interface. I wanted to see how density changes with position at different
>> pressures...I have the equilibrated boxes at several pressures obtained
>> from NPT but I am not sure whether running g_density on the current
>> simulations cells provides the profile I am after. Do you have any clue
>> whether or not the cell has to be extended in one direction to obtain the
>> density profile?
>>
>>
> If you're trying to produce an air-water interface, then indeed you will
> need some model for air within the unit cell, but there are several
> practical problems with that.  The first is that g_density does not deal
> well with changing box vectors, and the density profiles it produces under
> an NPT ensemble are incorrect (outstanding bug that needs to be fixed,
> IIRC).  The second is that if you run a simulation under NPT with void
> space, the unit cell will just compress down until there is no empty space.
>  Probably the best solution would be to equilibrate under NPT at the
> desired conditions, then build a new unit cell and run under NVT.  Using
> NVT will circumvent both problems, and if the proper pressure, density, etc
> have already been achieved, then you've got what you're after.
>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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