[gmx-users] [Fwd: PME & Temperature Coupling]

[David]

-----Forwarded Message-----
From: ali.hassanali.1 <hassanal at purdue.edu>
To: spoel at xray.bmc.uu.se
Subject: PME & Temperature Coupling
Date: Mon, 25 Oct 2004 21:28:48 -0500


Hello Everyone,

I am simulating a tri-peptide (Lys-Trp-Lys) in water where the tryptophan
is excited from its ground state to excited state charge distribution
after a certain time. I was initially using temperature coupling
with nose-hoover which yielded reasonable results but the tri-peptide
was not tumbling which is what one should expect. I then got rid of
temperature
coupling and sure enough it was making some sort of tumbling motion
but the temperature of the system increased drastically from 300 to about
800. I then tried
doing coupling on the water only but then the tumbling stopped.
I looked on the mailing list and someone suggested the use of PME which
I tried but the temperature is till increasing (at a slower rate).
Lowering
the neighbour list value didn't make much of a difference either (which
was another suggestion on a previous mailing list). Here is my mdp file.
Any suggestions, ideas will be appreciated. I want to have no temperature
coupling
but to get good dynamics and not have the potential and kinetic energy
explode which
is what currently happens. I have about 800 waters in the system.


         File: 1J9N-solv.mdp

title                    = Polymer_Simulation
cpp                      = /lib/cpp
include                  = -I../top
define                   =
integrator               = md
dt                       = 0.0001
emstep                   = 0.01
emtol                    = 1000
nsteps                   = 500000
nstxout                  = 2000
nstvout                  = 2000
nstfout                  = 2000
nstlog                   = 2000
nstenergy                = 250
nstxtcout                = 250
xtc_grps                 = Protein
energygrps               = Protein
nstlist                  = 3
ns_type                  = grid
rlist                    = 0.5
coulombtype              = PME
rcoulomb                 = 1.4
rvdw                     = 0.8
tcoupl                   = no
Pcoupl                   = no
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529
constraints              = all-bonds
lincs_iter               = 5
fourierspacing           = 0.15
optimize_fft             = yes


Thanks,

Ali

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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