its very hard to say what's going on, but for sure you should not use 10fs
time step. try 1fs, or perhaps 2fs if you are brave.
On Tue, Mar 31, 2009 at 4:49 AM, Aravind S <amm07bi007.students.amrita.ac.in
> wrote:
> Dear Sir,
> I have an other issue that has cropped up when I tried to simulate
> 227d.pdb.
> I was trying to simulate 227d.pdb with the following parameters: there are
> no constraints involved. I ran the 50 ps simulation with a 10fs time step,
> temp remaining constant at 300K. By default my ntx=7 and irest=1. My .rst
> file used was the result got through my previous simulation.
> My problem is that the .rst file isnt being generated , only the .mdcrd and
> the .out files got generated and the .mdcrd files had nothing written on
> it.
> The error in the .out file showed in the results section...
> the error read:--- Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 5 19 21
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> I would be highly obliged if somebody could solve this problem of mine.
> thank you
>
> Aravind
> ----- Original Message -----
> From: "Carlos Simmerling" <carlos.simmerling.gmail.com>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Sent: Monday, March 30, 2009 5:00:58 PM GMT +05:30 Chennai, Kolkata,
> Mumbai, New Delhi
> Subject: Re: [AMBER] .rst file generation problem.
>
> when restarting after minimization you need to set ntx=1 and irest=0 in
> your
> mdin file.
> there are no velocities in minimization so the next step cannot read them.
>
> 2009/3/30 Aravind S <amm07bi007.students.amrita.ac.in>
>
> > Dear Users,
> >
> > 1. I had a DNA complex(227.pdb), held fixed with a 500 Kcal/mol restraint
> > and minimized for 1000 cycles.
> > 2. This was followed by a 25ps MD to warm up the system from 100K to 300K
> > with DNA held fixed with a 100 Kcal/mol restraint and a 1fs time step.
> > 3. The system was further equilibrated by 25ps of MD at 300K, with the
> > restraint on the complex reduced to 50 Kcal/mol and using a 2fs time
> step.
> > 4. Further I ran a 5-step minimization protocol, each of the 1000 steps,
> > was then used with the restraint gradually reduced by 5 Kcal/mol
> > progressively, while starting with a 25Kcal/mol restraint.
> > 5. Finally, the system was created from 100K to 300K using a 10ps MD
> > simulation with no harmonic restraints on the complex.
> >
> > In this experiment, in the first 4 steps I have successfully generated
> all
> > the output files (.out),(.rst) and (.mdcrd).
> >
> > The .rst file that i had got in the 1st step(minimization), I used it in
> > the second step and so on...
> >
> > PROBLEM: My problem was in the final step wherein I ran the simulation
> for
> > 5000 steps, here the simulation got over in a fraction of a
> > second(considering my system to be a Pentium 4) and further on the .rst
> and
> > the .mdcrd files were not generated.
> > I opened my output file and an error message was displayed.
> >
> > The error message read: FATAL: Could not read velocities from
> > dna_wat_4min5.rst
> >
> > dna_wat_4min5.rst :- This was the .rst file generated during the final
> step
> > of the 5-step minimization protocol.
> >
> > I have attached the input and the output files of the final simulation
> and
> > .rst file of the previous minimization step.
> >
> > The command that I used for the final step of simulation is:-
> >
> > ./sander -O -i dna_wat_mdfiinal.in -o dna_wat_mdfiinal.out -p
> > dna_wat_prmtop -c dna_wat_4min5.rst -r dna_wat_mdfiinal.rst -x
> > dna_wat_mdfiinal.mdcrd -ref dna_wat_4min5.rst
> >
> > I would be very thankful if anyone could solve this problem of mine.
> >
> > ThankYou
> >
> > Aravind S
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 01 2009 - 01:14:04 PDT
