AMBER Archive (2008)

Subject: Re: AMBER: problems with restart of MD

From: Vijay Singh (vijayratan.singh_at_gmail.com)
Date: Sun Jan 13 2008 - 13:53:11 CST

Thanks Yong,

     Although I may not necessarily need the presence of the 3 ions, but I
am anyway persisting with them to have maximum consistency. All my other
results have these ions incorporated.

     I will probably do both - removal of the center of mass motion as well
as invoke PBC and compare them both.

Thanks again,
Vijay

On Jan 13, 2008 1:08 PM, Yong Duan <duan_at_ucdavis.edu> wrote:

>
> Physically, this is caused by entropy, something that we do not want to
> run against :).
>
> You were running gb simulations with 3 ions in an infinitely dilluted
> environment where "water" is modeled by GB. If everything is modeled
> accurately, this effectively mimicks a water box of infinite size (inifinte
> as the size of the universe :)). Imagine a full bucket (say, 1 gallon) of
> water and you add ONE protein molecule and add 3 ions. Do you expect them to
> stay together? At extremely low T, they might. At room T, they should not.
> At 800K, as is the case in your simulation, they should simply fly away from
> each other. This is not necessarily due to repulsive energy (as in
> electrostatic or van der Waals), but most likely due to entropy, despite the
> fact they might be attracted to each other by the electrostatic force.
> Entropy is something that we all have to live with when T is not zero. Yet,
> we all tend to forget about it.
>
> How to solve the problem? You need to add periodic boundary condition to
> mimick adequate ion/protein concentration if you really need those three
> ions. If, on the other hand, those three ions can be removed, or you don't
> want to play with the code, remove them.
>
> yong
> -----Original Message-----
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Vijay Singh
> *Sent:* Sunday, January 13, 2008 7:45 AM
> *To:* amber_at_scripps.edu
> *Subject:* Re: AMBER: problems with restart of MD
>
> 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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