AMBER Archive (2006)

Subject: Re: AMBER: 'lastrst' error for amber8

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Sep 13 2006 - 10:28:16 CDT

Also, note, if PMEMD supports the functionality you require, you should be
able to run using pmemd without hitting this sort of problem; the code is
written differently in order to be able to hand density fluctuations in a
multiprocessor run.
Regards - Bob Duke

----- Original Message -----
From: "michael crowley" <crowley_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Wednesday, September 13, 2006 11:14 AM
Subject: Re: AMBER: 'lastrst' error for amber8

> Dear Arvind,
> This is an unfortunately vague error message, and there is a way to fix
> the code so that this failure does not occur, but I have been somewhat
> reluctant to "fix" the problem since it usually indicates that there is a
> problem with the system, not with the program.
>
> Take a close look at your system and see if it is, in fact, inhomogeneous.
> Does it have vacuous regions? Before looking, use ptraj to image the
> solvent back into the primary unit cell.
> Also look at the density reported by sander to determine if it is
> reasonable (very near 1.0 for most solvated biomolecular systems).
> If it is inhomogeneous, then please let me know if you want to run the
> system this way. Normally people do not want vacuum bubbles in their
> systems, an artifact of the setup procedure coupled with not equilibrating
> at constant pressure long enough to reach a reasonable density.
>
> You can test that the problem is not with sander by running on one
> processor. Your results from a few steps will look reasonable, at least
> compared to the last frame of the runs you say are successful. On one
> processor, the inhomogeneous problem does not stop the simulation.
>
> If, in fact, your system is inhomogeneous, AND you do want to run that
> way, I can help to modify sander to run for you on 8 processors.
>
> Otherwise you will need to equilibrate to the correct density/volume
> before running for multiple nanoseconds, and throw away the other results.
>
> Best wishes
> Mike
>
>
> Arvind Marathe wrote:
>> Dear amber users,
>> I am running molecular dynamics simulations on a system of 25544 atoms. I
>> had already finished 5 ns simulation without any problem. After analysing
>> those results, when i tried to continue the simulation on the same
>> cluster
>> (SGI_ALTIX, 8 processors), i am getting the following error in my .out
>> file (please see below) which says 'exceeding lastrst in get_stack'. So
>> after searching the archives, i set the lastrst value to a very large
>> number (1000000000000) in my .in file and tried to run the simulation,
>> but
>> with the same error message. Just to check, i tried to run the simulation
>> with a previous restart file for the same biological system which had run
>> succesfully earlier on the same cluster. But even this effort to repeat
>> the previous run failed. Also note that other users are able to run their
>> amber8 jobs on the same cluster (with other biological systems) without
>> getting this error. Any ideas about what and where the problem could be?
>>
>> Thanks and Regards,
>> Arvind
>>
>>
>> Error in .out file
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>> --------------------------------------------------------------------------------
>> 4. RESULTS
>> --------------------------------------------------------------------------------
>>
>> ---------------------------------------------------
>> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
>> using 5000.0 points per unit in tabled values
>> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>> | CHECK switch(x): max rel err = 0.3338E-14 at 2.509280
>> | CHECK d/dx switch(x): max rel err = 0.8261E-11 at 2.768360
>> ---------------------------------------------------
>> | Local SIZE OF NONBOND LIST = 912907
>> | TOTAL SIZE OF NONBOND LIST = 7141631
>> ***** Processor 0
>> ***** System must be very inhomogeneous.
>> ***** Readjusting recip sizes.
>> In this slab, Atoms found: 25544 Allocated: 5108
>>
>> Exceeding lastrst in get_stack
>> lastrst = 799562
>> top_stk= 731432
>> isize = 136232
>> request= 867664
>> Increase lastrst in the &cntrl namelist
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
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>
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