Fwd: conf file for coarse grained simulation

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Dec 14 2009 - 02:19:52 CST

In addition: in agreement with lack of clashes in the system
protein+bilayer, a minimization at const volume of protein_bilayer
(where periodicity and PME were suppressed, otherwise the same conf
input) went to completion, as shown by the final portion of log:

WRITING COORDINATES TO DCD FILE AT STEP 999
TIMING: 1000 CPU: 44.9428, 0.0582436/step Wall: 105.083,
0.0957175/step, 0 hours remaining, 7.194077 MB of memory in use.
PRESSURE: 1000 0 0 0 0 0 0 0 0 0
GPRESSURE: 1000 0 0 0 0 0 0 0 0 0
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
       KINETIC TOTAL TEMP POTENTIAL
  TOTAL3 TEMPAVG

ENERGY: 1000 1565.9003 3628.5964 1222.6627
0.0000 -5623.0847 -22323.8166 0.0000
0.0000 0.0000 -21529.7419 0.0000
-21529.7419 -21529.7419 0.0000

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000
WRITING COORDINATES TO DCD FILE AT STEP 1000
WRITING COORDINATES TO RESTART FILE AT STEP 1000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 1000
FINISHED WRITING RESTART VELOCITIES
REINITIALIZING VELOCITIES AT STEP 1000 TO 300 KELVIN.
TCL: Setting parameter numsteps to 10
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 10
CLOSING EXTENDED SYSTEM TRAJECTORY FILE
WRITING COORDINATES TO OUTPUT FILE AT STEP 10
CLOSING COORDINATE DCD FILE
WRITING VELOCITIES TO OUTPUT FILE AT STEP 10
====================================================

WallClock: 107.425102 CPUTime: 46.286892 Memory: 6.857834 MB
Charmrun> Graceful exit.

Is anything special to be set in the conf file for minimization once
the system is solvated with cg water? I mean to prevent cg water
creating clashes, or anyway entering sites where it should not.

thanks

francesco

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Sun, Dec 13, 2009 at 10:08 PM
Subject: conf file for coarse grained simulation
To: NAMD <namd-l_at_ks.uiuc.edu>

I wonder whether for constant-volume coarse-grained minimization the
force field and force-field parameters are sufficiently set with:

# Input
paraTypeCharmm      on
parameters   /working_dir/rbcg-2007.par

# Force-Field Parameters
exclude 1-2
cutoff              35.0
switching           on
switchdist          20.0
pairlistdist        100.0
hgroupcutoff         0

I am looking for the causes that:

# Minimization
if {1} {
minimize            1000
reinitvels          $temperature
}

numsteps 10; # 300 ps 0.3 ns

systematically stops at step 536 for (I guess) too high potential energy:

WRITING COORDINATES TO DCD FILE AT STEP 535
PRESSURE: 536 4.37238e+07 -3.65202e+06 -603131 -1.20215e+06
5.36159e+07 1.62008e+06 -1.70818e+06 9.75259e+06 4.9599e+07
GPRESSURE: 536 4.37238e+07 -3.65202e+06 -603131 -1.20215e+06
5.36159e+07 1.62008e+06 -1.70818e+06 9.75259e+06 4.9599e+07
ENERGY:     536      1474.2549      6309.1780     11699.6826
0.0000          -2384.6469 187117483.7999         0.0000
0.0000         0.0000      187134582.2686         0.0000
187134582.2686 187134582.2686         0.0000       48979559.0521
48979559.0521   1178217.0000  48979559.0521  48979559.0521

Although superimposition of beads comes first to mind, the cg system
(protein+bilayer) is free of clashes, and was solvated with cg water.
I come from experience with Amber full atoms, where clashes are
eliminated by steepest descent + conjugate gradient minimization. Is
the minimizer of NAMD working differently or cg solvation has
introduced too hard a situation?

If I interpret correctly, the energy was not so high in the first
steps of minimization:

MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 2 3.45454e+12 1.69039e+12 -6.73379e+10 1.38241e+12
8.29396e+11 -4.76509e+10 -2.18147e+11 -2.94639e+11 1.62733e+11
GPRESSURE: 2 3.45454e+12 1.69039e+12 -6.73379e+10 1.38241e+12
8.29396e+11 -4.76509e+10 -2.18147e+11 -2.94639e+11 1.62733e+11
ENERGY:       2      1413.1771      6292.4622     11632.7598
0.0000          -2392.2611 9999999999.9999         0.0000
0.0000         0.0000      9999999999.9999         0.0000
9999999999.9999 9999999999.9999         0.0000      9999999999.9999
9999999999.9999   1178217.0000 9999999999.9999 9999999999.9999

thanks

francesco pietra

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:36 CST