I'm probalby doing something wrong but since neither the manual nor the
mailing list has driven me to the correct answer, i'm asking you the
problem. Thanks in advance for you answers and time.
I want to simulate my system with short NVT (for temperature
equilibration) and then NPT since i've observed that full NPT leads to a
delay in the temperature scaling (about 100ps is lost during this stage,
not that big, but i think this is because i'm not doing things correctly).
To set up the NVT calculation, i've just set pcoupl to no (as i think is
required), but *let* other pressure related parameters the same (i
assumed if pcoupl is off, pressure parameters are not taken into account).
I did 20 ps with my *supposed* NVT :
#####
; Pression, semiisotropic recommended for membrane simulations
Pcoupl = no
Pcoupltype = semiisotropic
tau_p = 10 10 ; see below for recommandations
ref_p = 1.0 1.0
compressibility = 4.5e-5 0
#####
I did the next NPT step for 10ps with parameters :
#####
; Pression, semiisotropic recommended for membrane simulations
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 10 10 ; see below for recommandations
ref_p = 1.0 1.0
compressibility = 4.5e-5 0
#####
Each run was done with gromp for generating the tpr + mdrun (for 4 nodes).
grompp->mdrun (4nodes) -> NVT, then
grompp (with NPT)
The problem is that running the second grompp returns me :
####
Opened ../pr1/fullmd_ions.edr as single precision energy file
Reading frame 40 time 20.000
-------------------------------------------------------
Program grompp_lam, VERSION 3.3.1
Source code file: enxio.c, line: 364
Fatal error:
Could not find energy term named 'Pcoupl-Mu-XX'
-------------------------------------------------------
####
Please note the same setup with full NPT (Pcoul Berendsen every time)
works ...
Thanks again for your comments and explanations.
Stéphane
--
Stéphane Téletchéa, PhD. http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901
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