AMBER Archive (2009)

Subject: Re: [AMBER] help with TIP4P and mpi pmemd

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Dec 03 2009 - 16:37:14 CST

Have you done this (tip4p) before? Try your prmtop/inpcrd/mdin with single
processor sander, then single processor pmemd, and then pmemd mpi. I bet
you have setup problems, or pmemd build problems, but this will sort that
out. I will let others expond on setting up an extra points simulation if
that is the problem. As an aside, why did you modify the elec and vdw
screening parms for 1-4 interactions, scnb and scee. This is I believe
generally not recommended, but maybe you are doing something I don't know
about... Also, do you really have two comment lines in front of &cntrl? I
have never tried that, maybe it is inconsequential but I don't know...
(because there are multiple reading passes, namelist i/o combined with group
i/o, I would not do anything nonstandard. May work fine, but namelist read
errors can be really obscure, especially in parallel - one reason to switch
to a single processor test case if something wierd happens.
Regards - Bob Duke
----- Original Message -----
From: "Hashem Taha" <hashemt_at_gmail.com>
To: <amber_at_ambermd.org>
Sent: Thursday, December 03, 2009 5:16 PM
Subject: [AMBER] help with TIP4P and mpi pmemd

>I have a problem with trying to run some jobs using TIP4P water as the
> solvent. I have tried running the same exact files with TIP3P water and
> the
> calculations started and completed perfectly. However, upon changing from
> TIP3P to TIP4P, my calculations would stop without reason. the file that I
> am trying to run is just a water minimization and it results in the
> following errors. The input file is also included below. The calculations
> start but after a few steps they come to a halt. Any help would be
> appreciated, and if you require further information please let me know...
>
> HT
>
> the errors are:
>
>>forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line
> Source
> pmemd 000000000048265A Unknown Unknown
> Unknown
> pmemd 00000000004777C3 Unknown Unknown
> Unknown
> pmemd 00000000004AA1D5 Unknown Unknown
> Unknown
> pmemd 00000000004CA1CE Unknown Unknown
> Unknown
> pmemd 000000000040744C Unknown Unknown
> Unknown
> libc.so.6 0000003F4D81D8B4 Unknown Unknown
> Unknown
> pmemd 0000000000407359 Unknown Unknown
> Unknown
> rank 7 in job 55 compute-0-8.local_45343 caused collective abort of all
> ranks
> exit status of rank 7: killed by signal 9
>
> the input file...
>
> Constant Volume Minimization
> # Control section
> &cntrl
> ntwx = 50, ntpr = 1, ntwr = 1,
> scnb = 1.0, scee = 1.0, nsnb = 25, dielc = 1, cut = 8.0,
> ntb = 1,
> maxcyc = 1000, ntmin = 0, dx0 = 0.01, drms = 0.0001,
> ntp = 0,
> ibelly = 0, ntr = 1,
> imin = 1,
> &end
> Group Input for restrained atoms
> 5.0
> RES 1 2
> END
> END
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>
>

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