AMBER Archive (2009)

Subject: Re: [AMBER] RE:xleap problem

From: oguz gurbulak (
Date: Thu Jan 29 2009 - 09:53:30 CST

Dear D Case and M. L. Dodson,

*Thank you* very much for your advices. It *works well* after using the set
command in LEaP to add the box information. And I run a min and then run a
constant pressure PME dynamics (1 atm ). I plotted the density over the
trajectory. The density must be 0.7636 g/ml. The and files are
in below. I attached the density graph to the mail. I'm planning to run a
constant volume to equilibrate the temperature as you said to me. I want to
learn if the operations I did are true ? What do you think about that ? What
do you suggest to me ? And I also want to make analysis without using ptraj.
So I want to learn the structure of the output files ( restrt, mdcrd, mdvel,
mden ) and meaning of the colums and rows in the output files. Can I easily
learn the informations of the atom's xyz coordinates, velocities and
accelerations in any time step and pressure tensors ? Or Should I write a
script in order to get these informations ? And I want to ask a question.
For example

NSTEP = 2000 Density = 0.7636




 NSTEP = 2500 Density = 0.7689

I want to get the output informations for NSTEP = 2000 in target Density =
0.7636 for input and start a md with little time steps. Is it possible to do
this in Amber? If so, what should I do to do this operation ?

Thanks in advance.

initial minimization








ntc=2, ntf=2,


MD equilibration


imin=0, irest=0, nstlim=5000000, dt=0.002, ntx=1,

ntc=2, ntf=2, ntpr=2000, ntwx=2000, ntwr=2000,

cut=9.825, ntb=2, ntp=1, ntr=0, ntt=1,tautp=2.0,

tempi=0.0, temp0=273.0, pres0=1.0, taup=2.0,


2009/1/27 David A. Case <>

> On Mon, Jan 26, 2009, oguz gurbulak wrote:
> > I'm now on Windows so I can only use rar or zip format for
> > compressing files.
> This is hardly true....just Google for "gzip windows" for example.
> > the mail. I used packmol in order to get my pdb file that includes 100
> > n-dodecane molecules. I added TER cards between each seperate n-dodecane
> > molecule with using a script. You can examine my packmol pdb file
> attached
> > to the mail.
> You need to use the "set" command in LEaP to add the box information
> after you load the packmol pdb file.
> Also note: a box size of 9 Ang or so is too small for Amber. The box
> size has to be at least twice the cutoff, so as a practical matter, the
> smallest box that really works is about 18 Ang.
> ...dac
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