AMBER Archive (2008)

Subject: Re: AMBER: problems with restart of MD

From: Vijay Singh (vijayratan.singh_at_gmail.com)
Date: Sun Jan 13 2008 - 09:45:25 CST

This problem occurred after 40ns. But on an earlier occasion it occurred
even at 10ns. In amber9 nscm=1000 is set as default, isn't it? Does that
mean that even when not specified, nscm=1000 ? I will goahead and try this
and maybe another with smaller value of nscm.

I don't have have water in my simulation but I do have have ions - 3 Na+.

Thanks a lot for your response

Regards,
Vijay

On Jan 12, 2008 9:58 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Hi Vijay,
>
> Here's the problem - line 488: 174.1520850 -
> 93.25969211280.4501416************-208.2782643************
>
> Your coordinates have increased so that they no longer fit in the space
> allocated for them in the file and it prints *'s. If you run this in serial
> it will probably quit with an error about problems doing formatted read but
> in parallel sometimes things can just hang. If you find weird errors in
> parallel it is always best to rerun in serial interactively so any errors
> are not "lost".
>
> How long has your simulation been running at this point? Normally it takes
> at least 50ns or so for things to have diffused far enough to cause the
> above problem. If your simulation time is much less than this then you could
> have problems that are causing your system to blow up.
>
> I would recommend going back to the previous restart file (that doesn't
> have star's in it) and rerun the simulation but this time set nscm=1000
> which will remove center of mass motion and stop your system translating
> through space. However, the fact that line 489 has:
>
> 1867.9560045-227.8549628 617.5614458
> while everything else is around:
>
> 337.8596051 341.2630291-537.0048903 337.8908765 342.2356117-536.7168717
> It suggest to me that some part of your system has took off and translated
> a long way away. You don't have ions or water here do you?
>
> I would both check on your system - perhaps run from the restart with
> ntwx=1 for a few hundred steps and visualize it to see what is happening.
> Also make sure you have nscm set or you will still have problems later when
> the entire system ends up translating too far due to center of mass motion
> imparted by having a thermostat present.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_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.
>
>
> ------------------------------
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Vijay Singh
> *Sent:* Saturday, January 12, 2008 01:49
> *To:* amber_at_scripps.edu
> *Subject:* Re: AMBER: problems with restart of MD
>
> Dear Dr.Ross,
>
> The results continues to be same even with NTX = 5. The error log
> file shows the following -
>
>
> forrtl: severe (64): input conversion error, unit 9, file
> /mnt/home/singhvij/mdout800_1.rst
> Image PC Routine Line Source
> sander.MPI 00000000007E2492 Unknown Unknown
> Unknown
> sander.MPI 00000000007E1692 Unknown Unknown
> Unknown
> sander.MPI 0000000000798246 Unknown Unknown
> Unknown
> sander.MPI 000000000074D63E Unknown Unknown
> Unknown
> sander.MPI 000000000074CC5A Unknown Unknown
> Unknown
> sander.MPI 000000000076D3A9 Unknown Unknown
> Unknown
> sander.MPI 00000000004F4556 Unknown Unknown
> Unknown
> sander.MPI 00000000004B8854 Unknown Unknown
> Unknown
> sander.MPI 00000000004B2BAD Unknown Unknown
> Unknown
> sander.MPI 0000000000405E32 Unknown Unknown
> Unknown
> libc.so.6 00002BA629E1A154 Unknown Unknown
> Unknown
> sander.MPI 0000000000405D6A Unknown Unknown
> Unknown
> forrtl: error (78): process killed (SIGTERM)
> Image PC Routine Line Source
> sander.MPI 000000000073763F Unknown Unknown
> Unknown
> sander.MPI 0000000000736740 Unknown Unknown
> Unknown
>
>
>
> I have no idea of how to proceed from here.Incase needed, I am attaching
> the "mdout800_1.rst" file for your perusal.
>
> Thanks a lot,
> Vijay
>
>
>
>
>
>
>
>
>
>
> On Jan 11, 2008 3:04 PM, Vijay Singh <vijayratan.singh_at_gmail.com > wrote:
>
> > Hi,
> >
> > Thanks for the response. I actually tried NTX = 5 too. Result was
> > same as that with NTX=7. But, I will go ahead and try once again and may be
> > wait a little more longer to see if the output file updates properly.
> >
> > Thanks again,
> > Vijay
> >
> >
> > On Jan 11, 2008 2:56 PM, Ross Walker < ross_at_rosswalker.co.uk> wrote:
> >
> > > Hi Vijay,
> > >
> > > The issue is that you are running a non-periodic simulation here
> > > (ntb=0) but when you restart you are setting ntx=7 which tells sander to
> > > expect box information from the input coordinate file. Since your input
> > > coordinate file does not have any box info the code is hanging there waiting
> > > for that information to be appended to the file. I realize we should
> > > probably find a better way to do this in the code so it fails gracefully
> > > rather than just hanging but this isn't always easy in parallel.
> > >
> > > Anyway, to answer your problem set ntx=5 and everything should be
> > > good. Also note that with Amber 9 you can always set NTX=5 and it will auto
> > > load the box info if you are running a periodic simulation. Thus ntx=7 is
> > > actually deprecated as an option hence why it is no longer in the manual.
> > >
> > > All the best
> > > Ross
> > >
> > > /\
> > > \/
> > > |\oss Walker
> > >
> > > | Assistant Research Professor |
> > > | San Diego Supercomputer Center |
> > > | Tel: +1 858 822 0854 | EMail:- ross_at_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.
> > >
> > >
> > > ------------------------------
> > > *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> > > Behalf Of *Vijay Singh
> > > *Sent:* Friday, January 11, 2008 09:30
> > > *To:* amber_at_scripps.edu
> > > *Subject:* AMBER: problems with restart of MD
> > >
> > > Hi,
> > >
> > >
> > > Not sure if my messages are reaching the right destination. I did not
> > > get any response on 2 different occasions earlier. Neverthless, another try.
> > >
> > > I am using amber9 and doing some very basic MD.I am having some
> > > trouble with the restart of MD production run. Not sure where I am going
> > > wrong. After initial minimization, the first part of run is fine
> > >
> > > The input files looks -
> > >
> > >
> > > &cntrl
> > > imin = 0, ntb = 0, irest = 0,
> > > igb = 1, ntpr = 10000, ntwx = 1000,
> > > ntt = 3, gamma_ln = 1.0,
> > > temp0 = 800.0,tempi = 800.0,
> > > nstlim = 40000000, dt = 0.001,
> > > cut = 999
> > > /
> > >
> > > mpiexec $AMBERHOME/exe/sander.MPI -O -i md_800k_1.in -o md800_1.out
> > > -c t57c_min.rst -p t57c.prmtop -r mdout800_1.rst -x mdout800_1.mdcrd
> > >
> > >
> > > Till this point I get all the output as needed. But the 2nd step
> > > below is where I get stuck on the restart part, the input is as follows -
> > >
> > >
> > > &cntrl
> > > imin = 0, ntb = 0, irest = 1, ntx = 7,
> > > igb = 1, ntpr = 10000, ntwx = 1000,
> > > ntt = 3, gamma_ln = 1.0,
> > > temp0 = 800.0,
> > > nstlim =40000000, dt = 0.001,
> > > cut = 999
> > > /
> > >
> > > #mpiexec $AMBERHOME/exe/sander.MPI -O -i md_800k_2.in -o md800_2.out
> > > -c mdout800_1.rst -p t57c.prmtop -r mdout800_2.rst -x mdout800_2.mdcrd
> > >
> > >
> > > From here I don't get any output. The mdout file stops with -
> > >
> > > Langevin dynamics temperature regulation:
> > > ig = 71277
> > > temp0 = 800.00000, tempi = 0.00000, gamma_ln= 1.00000
> > > | INFO: Old style inpcrd file read
> > >
> > > ----------------------------------------------------------------------------
> > > ----
> > > 3. ATOMIC COORDINATES AND VELOCITIES
> > > ----------------------------------------------------------------------------
> > > ----
> > >
> > >
> > > Could someone please help me on that.
> > >
> > > Regards
> > > Vijay
> > >
> > >
> >
>

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