Re: conf file for coarse grained simulation

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Dec 14 2009 - 19:15:57 CST

Hi Francesco,
it sounds like you're having problems with your cg water placement,
given the energies that you're getting. Could you post the exact
solvation parameters that you used?
Best,
Peter

Francesco Pietra wrote:
> 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 - 15:51:47 CST