Hi Paul
Thanks for this info. I will email you offlist to get the files.
All the best
Ross
> -----Original Message-----
> From: Paul Mortenson [mailto:P.Mortenson.astex-therapeutics.com]
> Sent: Thursday, August 26, 2010 2:33 AM
> To: AMBER Mailing List
> Cc: David Power
> Subject: Re: [AMBER] simulation of a restrained protein fragment
> +pmemd.cuda issues
>
>
> Hi Ross / Sasha,
>
> I have also seen this problem while taking part in the nvidia GPU Test
> Drive program that Ross mentioned a couple of weeks back. I have just 1
> group of restrained atoms, although it is quite large (2634 atoms - all
> heavy atoms in the protein). I see very similar behaviour - the cuda
> executable seg faults after a few seconds, but standard pmemd completes
> the job just fine. I have all the relevant files, but they're a little
> big to post to the list - Ross, please let me know if you would like me
> to send those to you separately (about 3MB zipped).
>
> Thanks to nvidia and their partners (Viglen in my case) for setting up
> the GPU Test Drive program. I found the system very straightforward to
> use, Viglen were helpful and responded very quickly to my emailed
> queries, and now I have the numbers I need to decide if a GPU system is
> going to work for us. Thanks also to any of the AMBER guys on this list
> who helped with this endeavour.
>
> Cheers,
> Paul
>
> -----Original Message-----
> From: Ross Walker [mailto:ross.rosswalker.co.uk]
> Sent: 25 August 2010 19:29
> To: 'AMBER Mailing List'
> Subject: Re: [AMBER] simulation of a restrained protein fragment
> +pmemd.cuda issues
>
> Hi Sasha,
>
> > First, pmemd and pmemd.cuda don't seem to accept restraintmask
> keyword
> > (sander works fine), and only read residue groups specified after the
> > parameter list.
>
> Yes this is, unfortunately, true. It would be great to have the
> restraintmask keyword added to pmemd, it is just a case of someone
> finding
> the time to do it. For the moment there is a program called ambmask in
> $AMBERHOME/bin which will convert a mask to the old style group input
> for
> you.
>
> > The initial minimization runs fine, with the entire protein
> restrained
> > (pmemd.cuda works).
> > The problems begin when multiple residue sets are restrained at the
> > second stage of minimization (protein is relaxed along with the
> > solvent). The full set of residues to be restrained is in the format
> > below:
> > Set 1
> > 1000.0
> > RES 1
> > END
> > Set 2
> > 1000.0
> > RES 24 43
> > END
> > ...
> > END
> > There is a total of 12 residue groups.
>
> This is way more complicated than any restraint setup I have tried so I
> am
> not surprised there is a bug in the GPU version of the code. Can you
> possibly send me (offlist) your prmtop, inpcrd and mdin file so I can
> take a
> look at this myself.
>
> One other thing to try. Can you try putting the whole lot in a single
> group?
> I.e. if you are keeping the force constant the same I think you can
> specify
> it in the same group. I don't have the syntax to hand right now but I
> thinking it is either:
>
> set 1
> 1000.0
> RES 1 1 24 43
> END
> END
>
> or
>
> set 1
> 1000.0
> RES 1
> RES 24 43
> END
> END
>
> Or something similar to that. Possibly. I am just thinking off the top
> of my
> head. If you can figure out the syntax and this works then it will help
> narrow down where the bug lies.
>
> > pmemd.cuda fails. When I work my way backwards by removing residue
> > groups, I get alternating segmentation faults and "unspecified launch
> > failure launching kernel kNLClearCellBoundaries" errors. Finally, at
> > only the first 3 residue groups it starts working and finishes the
> > minimization. Not sure how to explain that.
>
> One, unrelated thing to note, is that 1000 Kcal/mol/A^2 is a VERY large
> restraint. Something like 10.0 would be better and should be enough to
> keep
> things fixed. 1000 is fine for minimization but such a large restraint
> for
> MD (3 times the stiffness of a bond) will cause very high oscillations
> which
> could lead to integration errors.
>
> > Are there some unfinished issues with pmemd.cuda that affect
> restraints
> > handling?
>
> There are now. :'(
>
> > (all 12 groups with pmemd), I'm trying to run heating. At this point,
> I
> > use the same set of constraints and this command line:
> > /data/amber11/exe/pmemd.cuda -O -i wat_heat.in -o
> complex_wat_heat.out
> > -p complex_wat.prmtop -c complex_wat_min2.rst -r complex_wat_heat.rst
> -
> > x
> > complex_wat_heat.mdcrd -ref complex_wat_min2.rst
> >
> > pmemd.cuda generates a segmentation fault, while CPU version of pmemd
> > says "PMEMD terminated abnormally!" and leaves this message in the
> > output file:
> > Coordinate resetting cannot be accomplished,
> > deviation is too large
> > iter_cnt, my_bond_idx, i and j are: 1 444 869 870
> >
> > sander gives a similar complaint citing SHAKE not being able to run.
>
> This is because 1000 KCAl/mol/A2 is too much for your timestep since it
> gives very high frequency oscillations. Try 10.0.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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Received on Thu Aug 26 2010 - 05:00:05 PDT
