I would think you need the "ntwx = 1000" or other desired step frequency to
output the mdcrd file as well, since the default ntwx=0 will not output the
mdcrd trajectory.
I may be wrong on that, but I always have that flag.
Best,
Yuliana
On Mon, Apr 22, 2019 at 4:51 PM Alen Ahmetovic <alen2.mail.usf.edu> wrote:
> Hi Casalini,
>
> It looks to me like you forgot the negative sign in your ntwf flag. You
> wrote:
>
> Computing forces
> &cntrl
> imin=5,
> irest=1,
> ntx=5,
> ntwf=1,
> ioutfm=0,
> ntwprt=2000,
> ntb=2,
> ntp=1
> /
>
> Unless this in a typing error, I'm not sure otherwise. Sorry I couldn't be
> of more help.
>
> Best,
>
> Alen
>
> On Mon, Apr 22, 2019 at 3:54 PM Casalini Tommaso <
> tommaso.casalini.chem.ethz.ch> wrote:
>
> > Dear Amber users and developers,
> > I would like to compute the forces acting on a certain number of atoms in
> > my molecular trajectory.
> > In order to do this, I used sander with the following input file:
> >
> > Computing forces
> > &cntrl
> > imin=5,
> > irest=1,
> > ntx=5,
> > ntwf=1,
> > ioutfm=0,
> > ntwprt=2000,
> > ntb=2,
> > ntp=1
> > /
> >
> > I run sander with the appropriate flags, indeed everything goes smoothly
> > and the computed energies make sense (I compared them with the previously
> > obtained values from the simulations). Anyway, the file "forces.mdcrd"
> > where I wanted to store the computed forces is empty.
> > I had another look at the manual, which states:
> >
> > "Every ntwf steps, the forces will be written to the mdfrc file. If ntwf
> =
> > 0, no force trajectory file
> > will be written. If ntwf = -1, forces will be written to the mdcrd, which
> > then becomes a combined
> > coordinate/force trajectory file, at the interval defined by ntwx. This
> > option is available only for binary
> > NetCDF output (ioutfm = 1)."
> >
> > At this point, it is not clear to me whether the ntwf-not-equal-to-zero
> > option is compatible only with ioutfm = 1 in every case, or if this is
> > strictly true only when ntwf = -1. Indeed, I obtained an empty file but
> > sander did not complain.
> >
> > My questions are the following:
> >
> > 1) Why did I obtain an empty file for the forces? Did I make some
> mistake,
> > or should I put ioutfm = 1?
> > 2) Assuming that I must set ioutfm = 1, I would like to have an ASCII
> > formatted file for the force, since I wrote a post-processing code in
> > matlab that can be "fed" with .mdcrd files. Can I make a Netcdf-to-ascii
> > conversion with cpptraj as I do for molecular trajectories?
> >
> > I thank you in advance for your help and support.
> > With my best regards,
> > Tommaso
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
Yuliana Bosken
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Received on Mon Apr 22 2019 - 21:00:02 PDT
