Re: Re: Simulated Annealing Config

From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
Date: Tue May 24 2005 - 14:55:49 CDT

Hello !!!!

I have a NPT .conf, taken from NAMD tutorials. I wanted to begin my
simulation increasing temperature slowly from 100 K to 310 K , and
then mantain temperature. So I modify Jerome's script

# Minimization
minimize 100
reinitvels $temperature

run 500

for { set TEMP 105 } { $TEMP < 310 } { incr TEMP 5 } {
            langevinTemp $TEMP
            langevinPistonTemp $TEMP
        run 500
}

langevinTemp 310
langevinPistonTemp 310

## Equilibrium at 310K
run 250000

I put langevinPistonTemp inside the for loop because I am using
constant presure. The first 500 steps above the loop ran well,
nevertheles inside the loop the following error message appear in the
output:

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 500
PRESSURE: 600 -138.577 -132.628 -13.9673 -132.628 -655.09 -119.74
-13.9673 -119.74 -18.8149
GPRESSURE: 600 -72.9549 -1.16532 51.9709 -148.195 -596.702 -153.193
-181.041 -92.0929 -39.5925
PRESSAVG: 600 1.07577 67.0278 30.6459 67.0278 -126.262 -55.374 30.6459
-55.374 154.997
GPRESSAVG: 600 -1.86664 68.5161 31.0215 71.273 -122.128 -46.8533
35.4172 -58.1341 153.583
ENERGY: 600 104.1790 350.0371 340.5935
18.7730 -56130.8032 5726.1828 0.0000
0.0000 3758.3035 -45832.7344 135.4386
-45820.2393 -45816.8959 138.3656 -270.8275
-236.4166 127505.2548 9.9370 9.8630

TCL: Setting parameter langevinTemp to 105
TCL: Setting parameter langevinPistonTemp to 105
TCL: Running for 500 steps
PRESSURE: 600 -135.588 -127.438 -19.1139 -127.438 -648.384 -123.346
-19.1139 -123.346 -19.1616
GPRESSURE: 600 -75.6802 -2.35405 52.7984 -149.383 -596.71 -152.745
-180.214 -91.6456 -37.7993
ENERGY: 600 104.1790 350.0371 340.5935
18.7730 -56130.8032 5726.1828 0.0000
0.0000 3757.9108 -45833.1271 135.4244
-45820.9839 -45816.5299 135.4244 -267.7113
-236.7298 127505.2548 -267.7113 -236.7298

Info: Initial time: 8 CPUs 0.167641 s/step 0.970143 days/ns 13118 kB memory
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

As in the .conf i attached is stated, useFlexibleCell is disabled. I
tested using a NVT dynamics (the same script with useGroupPressure=no
and langevinPiston=off) and it works, so the problem must come from
using langevinPiston=on. Does someone know how to do a Simulated
annealing with NPT????

Thanks


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