From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Aug 10 2011 - 01:21:10 CDT
Yes, but shouldn't he have seen that the simulations stopped to write output?? ^^
The begin of his minimization shew possible bad initial structure. Maybe your right, just restart, but before check structure.
Mit freundlichen Grüßen
Von: JC Gumbart [mailto:gumbart_at_ks.uiuc.edu]
Gesendet: Mittwoch, 10. August 2011 07:52
An: 'Norman Geist'; 'Kartheek'
Cc: 'Namd Mailing List'
Betreff: RE: namd-l: Minimization is taking a lot of computing time.
I think the minimization is hung, which happens sometimes. Try correcting errors in the initial structure and start again.
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Norman Geist
Sent: Wednesday, August 10, 2011 12:45 AM
Cc: Namd Mailing List
Subject: AW: namd-l: Minimization is taking a lot of computing time.
well timing says 0,48 s/step what sounds ok, maybe you will just have to wait. You should also know that namd doesn't converge and stop the minimization itself, it'll run till the supplied step count is reached. So in theory your simulation should took 19 minutes to finish. If it doesn't something is wrong. Have you compiled namd by yourself or is it a precompiled binary from the namd homepage. If self compiled, try the precompiled one maybe. Also you can set outputtiming little slower and look at the information which is printed then, maybe check if the timings are true. I have no explaination at the moment why your simulation tells half a second for one step but doesn't finish in hours. I also find that you have huge energys for vdw and pressure in comparision to bond and angle and also system size, maybe check this.
Mit freundlichen Grüßen
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Kartheek
Gesendet: Dienstag, 9. August 2011 13:07
Betreff: namd-l: Minimization is taking a lot of computing time.
Here i am providing an URL to access output file.
----- Original Message -----
From: "Kartheek" <kartheek.p_at_research.iiit.ac.in>
Sent: Friday, August 5, 2011 3:23:42 PM
Subject: Minimization is taking a lot of computing time.
Dear NAMD users.
I am started running a minimization for a system of nearly 16,060 atoms,minimization has been running since 48 hours on an eight processor system. Here is my configuration file.Some one please tell me what is the reason behind such a long minimization process.
Thanks in advance.
# periodic boundary conditions
cellBasisVector1 122.0 0.0 0.0
cellBasisVector2 0.0 42.0 0.0
cellBasisVector3 0.0 0.0 40.0
cellOrigin 0.1 0.2 0.2
xstfreq 600 # same as dcd freq
wrapwater on # off is default
wrapall off # off is default
# simulation space partitioning
margin 4.0 # 0.0 is the default value
# timestep parameters
timestep 1.0 # in femtoseconds
stepspercycle 24 # default
# basic dynamics
temperature 300.0 # initial temperature (K)
dielectric 1.0 # default
rigidbonds none # options : none,water,all
# PME parameters
pme yes # 'on' is also possible
# Multiple timestep parameters
# input files
coordinates ionized.pdb # PDB file
structure ionized.psf # Xplore PSF file
parameters par_all27_prot_na.inp # parameter file (CHARMM)
paratypecharmm on # (on or off) or (yes or no)
# output files
binaryrestart yes # default
dcdunitcell no # 'yes' is default if periodic cell is used
# standard output
# Temperature control
# Langevib dynamics parameters
#langevinpiston on # NVT(off), NPT(on)
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