Hi Ross,
Yes, u were right. There are **** parts in the md34.rst file. I will
follow your suggestion, but I have another question: I have used the last
traj. file created by the MD (md34.mdcrd) and extracted the coordinates of
the last trajectory point. That .rst file does not have any *** in it, and
yet it does not work to run the simulation. It is giving the following
error message:
[yildirim.anatolia ~/analyze_arde_results]# forrtl: severe (174): SIGSEGV,
segmentation fault occurred
Image PC Routine Line Source
sander 081825C4 Unknown Unknown Unknown
sander 0817BD8E Unknown Unknown Unknown
sander 08418024 Unknown Unknown Unknown
sander 0812A4CE Unknown Unknown Unknown
sander 081181CD Unknown Unknown Unknown
sander 08114BA5 Unknown Unknown Unknown
sander 0804A871 Unknown Unknown Unknown
libc.so.6 B7B7C87C Unknown Unknown Unknown
sander 0804A7B1 Unknown Unknown Unknown
I just tried to do a simple minimization:
------------ min.in ------------
Deneme
&cntrl
imin=1, maxcyc = 200,
ntpr = 5,
ntr=0,
/
--------------------------------
The file is at
http://www.pas.rochester.edu/~yildirim/amber/md34.rst.new
I can create the a .pdb file using this .rst.new coordinate file, but it
wont work on the simulations. Any idea on why this is happening? Thanks.
Best,
On Tue, 12 Sep 2006, Ross Walker wrote:
> Hi Ilyas,
>
> Have you had a look at the restart file? I suspect that you have *******'s
> in there somewhere because your coordinates were too large to fit in the
> available space.
>
> Your only solution is to go back to the last restart file that worked,
> reimage this and then repeat the remainder of your simulation or
> alternatively go back to that restart file and then from then on choose to
> write binary restart files. NTXO = 1 and then ntx=6 on subsequent restarts.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
> > -----Original Message-----
> > From: owner-amber.scripps.edu
> > [mailto:owner-amber.scripps.edu] On Behalf Of Ilyas Yildirim
> > Sent: Tuesday, September 12, 2006 14:10
> > To: amber.scripps.edu
> > Subject: AMBER: forrtl: severe (64): input conversion error,
> > unit 9, file
> >
> > Dear All,
> >
> > I have been doing a long simulation. On the 47th ns. the
> > simulation just
> > stopped. I have a .rst file (md34.rst), but cannot continue on the
> > simulation. The error I am getting is the following:
> >
> > forrtl: severe (64): input conversion error, unit 9, file
> > /home/yildirim/igigicic_expl_icfe0_continued/md34.rst.old
> > Image PC Routine Line Source
> > sander.a8.paralle 081D62D6 Unknown Unknown Unknown
> > sander.a8.paralle 081D49A9 Unknown Unknown Unknown
> > sander.a8.paralle 081B5E41 Unknown Unknown Unknown
> > sander.a8.paralle 081806EE Unknown Unknown Unknown
> > sander.a8.paralle 0818041E Unknown Unknown Unknown
> > sander.a8.paralle 081949D2 Unknown Unknown Unknown
> > sander.a8.paralle 080DCACE Unknown Unknown Unknown
> > sander.a8.paralle 080DC6F1 Unknown Unknown Unknown
> > sander.a8.paralle 080ABF01 Unknown Unknown Unknown
> > sander.a8.paralle 080777BF Unknown Unknown Unknown
> > sander.a8.paralle 080772D2 Unknown Unknown Unknown
> > sander.a8.paralle 0804B365 Unknown Unknown Unknown
> > libc.so.6 557C5500 Unknown Unknown Unknown
> > sander.a8.paralle 0804B291 Unknown Unknown Unknown
> >
> > I cannot even create a .pdb file from this .rst file. I used the last
> > .mdcrd (md33.mdcrd) to get the last .rst file from this
> > trajectory file
> > (md34.rst.new). I CAN use this file to create a .pdb file, but it wont
> > work to continue the simulation. The md.in file I am using in the
> > simulations is the following:
> > -------------------- md.in --------------------
> > 1 ns simulation
> > &cntrl
> > imin=0,
> > ntx=5,irest=1,
> > ntpr=250,ntwr=1000,ntwx=2500,
> > ntc=2,ntf=2,ntb=1,cut=10,
> > igb=0,
> > ntr=0,
> > nstlim=1000000,dt=0.001,nscm=5000,nrespa=2,
> > ntt=3,gamma_ln=1,tempi=300,temp0=300,ig=666,
> > ntp=0,taup=2.0,pres0=1
> > /
> > -----------------------------------------------
> > Is this error related to AMBER, or Intel FCC? I will greatly
> > appreciate if
> > someone can help me on this. Thanks.
> >
> > Best,
> >
> > PS: I tried to attach the prmtop/inpcrd files, but the email
> > bounced back.
> > I put the files to the following place:
> >
> > http://www.pas.rochester.edu/~yildirim/amber
> >
> > --
> > Ilyas Yildirim
> > ---------------------------------------------------------------
> > - Department of Chemisty - -
> > - University of Rochester - -
> > - Hutchison Hall, # B10 - -
> > - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66
> > (Office) -
> > - http://www.pas.rochester.edu/~yildirim/ -
> > ---------------------------------------------------------------
> >
> >
> >
> > --------------------------------------------------------------
> > ---------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
>
>
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>
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Wed Sep 13 2006 - 06:07:18 PDT
