Re: System minimization: fail after 199 steps

From: Charles Danko (dankoc_at_gmail.com)
Date: Wed Nov 03 2004 - 11:53:06 CST

Hi,

Thanks to Brian and Dr. Valencia for their help.

The machines are a cluster of Sun SPARC 64 bit processors running
Solaris 7. I am using bsub for multithreading. My administrator may
let me run charm+ if you think that it may solve the problem, but
there may be some good reason that it wasn't used before (namd was
compiled by a colleague of mine, and I am not sure of specific issues
he faced when putting it together).

The system is a protein, lipid, and water system, in total, 58,236
atoms constructed from a protein homology model. The system was
assembled using VMD, the membrane 1.0 plug-in, and solvate 1.2 (to
solvate the top and bottom where the protein was sticking out of the
pre-equilibrated lipid-water system constructed by membrane). I
deleted all atoms within 1A of the protein and am now trying to
minimize the system.

Based on Dr. Valencia and Dr. Bennion's suggestions I changed the
script file. I adapted the one intended to heat the system after the
minimization. I have included the new script file as an attachment.
The run still crashes after 199 steps, but this time it returns a
malloc error. Short by 2GB?
The last part of the output is pasted below. Many of the forces are
positive again.

I have tried to fix the protein and minimize the water/lipids; the
output is pasted below. The system lasted for 299 steps this time,
but received the same malloc error.

I have NOT deleted the atoms which fall outside of my periodic
boundary. If you recommend I will do this and try to run the new
script again. I am acting under the assumption that these atoms will
be ignored.
Is this coorect?

Because the problem seems to be a memory allocation error, I am
thinking that the next step will to be trying to convince my
administrator to compile charm+.
Any thoughts or suggestions?
Do I need to recompile all of namd, or can I just compile charm+ without it?

Thanks again for all of the help,
Charles

Output files:

New script, no atoms fixed.

BRACKET: 6.57916e-07 652.946 -2.45009e+09 -8.45313e+07 9.29531e+08
ENERGY: 198 522579.9239 151303.8494 10858.5910 1446.8211
   -80557.5403 481695.6698 0.0000 0.0000 0.0000
  1087327.3149 0.0000 1087327.3149 1087327.3149 0.0000
   188642.4062 235104.9289 576000.0000 188642.4062 235104.9289

BRACKET: 1.6835e-07 70.1294 -8.45313e+07 1.17645e+07 9.29531e+08
ENERGY: 199 522585.2964 151303.6975 10858.5915 1446.8152
   -80557.4059 481690.3089 0.0000 0.0000 0.0000
  1087327.3036 0.0000 1087327.3036 1087327.3036 0.0000
   188639.2161 235101.2267 576000.0000 188639.2161 235101.2267

LDB: LOAD: AVG 231.478 MAX 291.895 MSGS: TOTAL 184 MAXC 20 MAXP 5 None
LDB: LOAD: AVG 231.478 MAX 255.756 MSGS: TOTAL 184 MAXC 20 MAXP 5 Alg7
LDB: LOAD: AVG 231.478 MAX 236.106 MSGS: TOTAL 184 MAXC 20 MAXP 5 Alg7
Could not malloc() 2118274080 bytes--are we out of memory?Fatal error, aborting.
Rtasks fail:
Rtask(s) 1 : exited with signal <6>
Rtask(s) 3 2 4 5 8 6 7 10 9 : exited with signal <15>
Rtask(s) 1 : coredump
>

New Script, Fixed Protein

BRACKET: 1.64649e-05 26875.6 -8.15248e+09 -2.11699e+09 7.56124e+09
ENERGY: 298 246811.3244 127002.1868 7801.5138 776.0334
  -110553.6799 343151.2350 0.0000 0.0000 0.0000
   614988.6135 0.0000 614988.6135 614988.6135 0.0000
   156657.9925 177933.1586 576000.0000 156657.9925 177933.1586

BRACKET: 8.23246e-06 12090.3 -2.11699e+09 -9.70546e+08 7.56124e+09
ENERGY: 299 245766.2529 126976.5313 7802.2252 775.5543
  -110592.3262 343704.2276 0.0000 0.0000 0.0000
   614432.4651 0.0000 614432.4651 614432.4651 0.0000
   156870.7170 178776.2517 576000.0000 156870.7170 178776.2517

LDB: LOAD: AVG 212.831 MAX 217.851 MSGS: TOTAL 184 MAXC 20 MAXP 5 None
LDB: LOAD: AVG 212.831 MAX 216.577 MSGS: TOTAL 184 MAXC 20 MAXP 5 Refine
Could not malloc()--are we out of memory?Fatal error, aborting.
Rtasks fail:
Rtask(s) 1 : exited with signal <6>
Rtask(s) 3 2 4 5 6 8 7 9 10 : exited with signal <15>
Rtask(s) 1 : coredump
>

On Tue, 02 Nov 2004 13:22:50 -0600 (CST), J. Valencia
<jonathan_at_ibt.unam.mx> wrote:
> Also, for par_all27_prot_lipid.prm the suggested cutoff scheme is:
> switchdist 10.0
> cutoff 12.0
> pairlistdist 14.0
> This is stated almost at the end of the file.
>
> Good luck!
>
> J. Valencia.
>


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