From: eprates_at_iqm.unicamp.br
Date: Thu Jan 15 2009 - 11:51:54 CST
Dear namd users,
I am simulating a system constituted of about 23000 atoms (water molecules
and one very small polimer - PEO of 8 monomers ).
After 4 ns of equilibration (NPT), I have run 250 ps in the NVE ensemble,
at 298 K. The problem is that the energy increased much more than a
resonable 0.5% of the initial value.
I have already read the previous messages about this subject, but even so,
I could not find out the cause to this problem.
Just bellow I copied the input file... Can anyone see a parameter that
could be the cause of this problem?
I thank you all in advance.
Érica T. Prates
# Molecular system
structure PEO-4_fim.psf
## Coordinates in PDB format
coordinates peo4-term1.out.coor
extendedsystem peo4-term1.out.xsc
velocities peo4-term1.out.vel
## Constrain all bonds including hydrogens
rigidbonds all
wrapall on
## Force field
paratypecharmm on
parameters par_PEO-4
exclude scaled1-4
1-4scaling 1.0
## Option short-range interaction approximations
switching on
switchdist 10.0
cutoff 15.0
pairlistdist 20.0
margin 0
stepspercycle 10
## Particle mesh ewald
pme yes
pmegridsizex 32
pmegridsizey 32
pmegridsizez 32
#(the length of the cubic box is of about 33 A)
## Output
outputenergies 100
outputtiming 100
outputPressure 100
binaryoutput no
imdon yes
imdfreq 1
imdport 3111
restartname peo4-din2
restartfreq 1000
outputname peo4-din2
dcdfreq 4
XSTfile peo4-din2.xst
XSTfreq 1000
## Integrator
timestep 1
run 250000
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