sure - I am using amber10 and ambertools 1.4 which should be the lastest.
On Mon, Sep 13, 2010 at 12:41 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> it's not possible to help unless you specify which version of sander and
> which version of ptraj/ambertools.
>
> On Mon, Sep 13, 2010 at 6:19 AM, Jorgen Simonsen <jorgen589.gmail.com
> >wrote:
>
> > Hi all,
> >
> > I have performed a remd with a 250.000 number of exchange trials during
> the
> > simulation every 0.5 ps. I have set ntwx=5.000 so I would expect 25.000
> > structures in my simulation but after processing the data using the
> script
> > to extract the coordinates at different temperatures I get
> >
> > #!/bin/csh
> >
> > ptraj l_dermorphin.prmtop << EOF
> > trajin remd.mdcrd.001 remdtraj remdtrajtemp 300.0
> > trajout remd.300K.mdcrd nobox
> >
> > distance d1 out dist.300K.dat :1.CA :7.CA
> >
> > go
> > EOF
> > which reads all the output files
> >
> > Processing AMBER REMD trajectory (new format) files remd.mdcrd.001 ->
> > remd.mdcrd.010
> >
> > I only get 19999 structures - when I grep *REMD*' in the mdcrd.001 file I
> > get 25.000 lines with REMD as expected. I do not know where my mistake is
> > any help appreciated
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 13 2010 - 04:30:03 PDT
