Hi Bongkeun
This is a known problem. It should be fixed very shortly with the same patch
that will enable parallel GPU runs.
In the meantime if you send me your prmtop, inpcrd and mdin file I will run
it with the development tree and check it works. Don't send it to the list
since messages above 2MB in size are not permitted.
I trust you have tried this with the CPU version of PMEMD and verified that
it is just a problem related to the GPU version.
All the best
Ross
> -----Original Message-----
> From: Bongkeun Kim [mailto:bkim.chem.ucsb.edu]
> Sent: Thursday, September 30, 2010 4:46 PM
> To: amber.ambermd.org
> Subject: pmemd.cuda error with group restraint
>
> Hello,
>
> I built a self assembled monolayer surface with explicit water.
> Its structure is dialkane sulfide.
> In MD simulation, I wanted to fix the position of the center sulfur
> atom in each monomer by using following input file.
>
> equil.in---------------------------------------
> sam water: 100ps MD
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10.0, ntr = 1,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 50000, dt = 0.002,
> ntpr = 1000, ntwx = 1000, ntwr = 1000
> /
> Fix S atoms
> 10.0
> FIND
> S * * LIC
> SEARCH
> RES 1 225
> END
> END
> -----------------------------------------------
>
> With sander or sander.MPI, it does work with selecting 225 sulfur atoms.
> -output file--------------------------------
> ----- READING GROUP 1; TITLE:
> Fix S atoms
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
> ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE
> INCLUDED IN GROUP BE
> LOW
>
> GRAPH NAME = S SYMBOL = * TREE SYMBOL = *
> RESIDUE TYPE = LIC
>
> GRP 1 RES 1 TO 225
> Number of atoms in this group = 225
> ----- END OF GROUP READ -----
> ------------------------------------------------------
>
> But if I run this with pmemd.cuda, I always have just a segmentation
> fault error.
> The command is
> --------------------------------------------------
> pmemd.cuda -O -i equil.in -p samch3w.prmtop -c samch3w_heat1.rst -r
> samch3w_equil1.rst -
> o samch3w_equil1.out -x samch3w_equil1.mdcrd -ref samch3w_heat1.rst -
> gpu 1
> ----------------------------------------------------------------
> In the input file, if the first argument is *, then pmemd.cuda works OK.
> But the problem is the first one is assigned to any letter.
> --------------->error
> FIND
> S * * LIC
> SEARCH
> ---------------> error
>
> --------------->works fine
> FIND
> * * * LIC
> SEARCH
> ---------------->works fine
>
> Do you have any idea why pmemd.cuda fails with this FIND SELECT
> statement?
> Thank you.
> Bongkeun Kim
>
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Received on Thu Sep 30 2010 - 18:00:03 PDT
