Re: COARSE GRAINED WATER MODEL

From: Valeria Marquez (valeria.marquez.m_at_gmail.com)
Date: Tue Oct 20 2009 - 10:16:04 CDT

Thank you in advance for your answer. When I told you about "atoms", I meant
"beads". I'm sorry about the confusion.

The simulation stops in the minimization step nš 199. This is the last line
I got in the log file :

ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 199 2964.9003 5521.2571 15751.8993
0.0000 -2381.6269 170580262.4472 0.0000
0.0000 0.0000 170602118.8770 0.0000 170602118.8770
170602118.8770 0.0000 15341394.4297 15341394.4297
3148200.0000 15341394.4297 15341394.4297

It seems VDW energy is too high.

I'm trying to follow your suggestion. I'm running a simulation using full
atom system, and I wonder it helps.

Maybe I'm doing something wrong with NAMD configuration file. I am not an
expert with NAMD configuration for CG systems:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------
paraTypeCharmm on
parameters rbcg-2007.par
temperature 310

exclude 1-2
cutoff 35.0
switching on
switchdist 20.0
pairlistdist 100.0
hgroupcutoff 0

timestep 2.0
rigidBonds none
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20

langevin on
langevinDamping 2
langevinTemp 310
langevinHydrogen no

langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 100
langevinPistonDecay 50
langevinPistonTemp 310

cellBasisVector1 180.0 00.00 00.00
cellBasisVector2 00.00 110.0 00.00
cellBasisVector3 00.00 00.00 159.0
cellOrigin 2.65 2.36 4.16

Pme on
PmeGridsizeX 182
PmeGridsizeY 112
PmeGridsizeZ 162

margin 6
-----------------------------------------------------------------------------------------------------

I appreciate your help.

Best wishes.

Valeria Marquez.

2009/10/20 Valeria Marquez <valeria.marquez.m_at_gmail.com>

> Hello everyone,
>
> I'm interested in working with a protein and water, using the coarse
> grained model. Previously, I built a CG protein model, using the VMD CG
> Builder. Later, I ran a vacuum simulation with NAMD, and I didn't have any
> problems.
>
> Now, I'd like to build a protein embedded in water, using the CG model.
> First, I built full atom protein and I placed it in a full atom water box--001485f912a840c79f04765f577c--

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