AMBER Archive (2005)

Subject: Re: AMBER: pmemd and restraints

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Jan 26 2005 - 11:45:01 CST

Filip -
The restraints stuff is supported and tested to some extent, but because
this is less used code, there is always the possibility of an error. If you
will make a tarball of all your input and send it to me, I will be glad to
determine if there is a problem with the code (and fix it), or if this is
"pilot error". I presume your mdin file does not really have the group
restraints at the top (I believe there at least used to be a restriction on
placement of this stuff; some mods were made in pmemd to make it more robust
in the face of disordered namelist input, but I am not sure off the top of
my head about being able to read restraints anywhere). Also, what version
of pmemd are you using?
Thanks - Bob Duke
(send tarball to rduke_at_email.unc.edu)

----- Original Message -----
From: "Filip Lankas" <filip.lankas_at_epfl.ch>
To: <amber_at_scripps.edu>
Sent: Wednesday, January 26, 2005 12:01 PM
Subject: AMBER: pmemd and restraints

>
> Hello Amber users,
>
> I have a problem running pmemd with position restraints and increasing
> temperature. The system is a piece of DNA with explicit ions and water,
> periodic, PME. My input file looks like this:
>
>
> Group input for DNA restraints: 25 kcal/mol.
> 25.0
> RES 1 24
> END
> END
> ***************************** md.in *****************************
> *************************************************************************
> Heating the system with 25 kcal/mol restraints on DNA, V=const
> &cntrl
> imin=0, ntx=1, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
> nscm=5000,
> ntf=2, ntc=2,
> ntb=1, ntp=0,
> nstlim=50000, t=0.0, dt=0.002,
> cut=9.0,
> tempi=100.0, ntt=1,
> ntr=1, nmropt=1,
> lastist=10000000
> &end
> Heating from 100 to 300 K
> &wt type='TEMP0', istep1=0, istep2=5000, value1=100.0, value2=300.0,
> &end
> &wt type='TEMP0', istep1=5001, istep2=50000, value1=300.0, value2=300.0,
> &end
> &wt type='END', &end
>
> ... the job starts, but crashes saying (in the stderr):
>
> lib-4001 : UNRECOVERABLE library error
> Encountered during a sequential formatted READ from unit 5
> Fortran unit 5 is connected to a sequential formatted text file: "md.in"
> Current format: 9208 FORMAT(20a4)
>
> Am I doing something wrong, or does pmemd simply not support this kind of
> task?
>
> Thank you in advance,
>
> Filip
>
>
>
>
>
> --
> ---------------------------------------------
> Dr. Filip Lankas
> Institute for Mathematics B
> EPFL (Swiss Federal Institute of Technology)
> Station 8
> CH-1015 Lausanne
> Tel: +41 21 693 2593 Fax: +41 21 693 5530
> ---------------------------------------------
>
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