[gmx-users] [Fwd: Different in Pressure]

[David van der Spoel]

-------- Forwarded Message --------
From: chiloo Laohpongspaisan <chiloo77 at yahoo.com>
To: spoel at xray.bmc.uu.se
Subject: Different in Pressure
Date: Sun, 14 Aug 2005 20:18:10 -0700 (PDT)
Dear Dr. David,
 
As you suggested, to use Gromacs 3.2.1 for continuing trajectory. It
seems to be good that all the energies and some properties are equal,
except pressure. You can see below that i mark the pressure value. Is it
significant ? and how can i do to adjust the pressure which will be
equal as the other properties. (And the next is my input file that i
use)  
 
the previous file
             Step           Time         Lambda
         500000     1000.00006        0.00000
   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.080067  14445  14446   0.025450
        After LINCS         0.000122    404    407   0.000008
   Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.
LJ-14
    2.00835e+04    2.56519e+03    4.14071e+03    8.06361e+02    3.94693e
+03
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coulomb (LR)
Potential
    1.95655e+04    1.31344e+03   -2.14504e+05   -1.01600e+05   -2.63682e
+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    4.58780e+04   -2.17805e+05    3.12032e+02    1.52697e+02
 
the 2nd file
Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.
LJ-14
    2.00835e+04    2.56519e+03    4.14071e+03    8.06361e+02    3.94693e
+03
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coulomb (LR)
Potential
    1.95655e+04    1.31344e+03   -2.14504e+05   -1.01600e+05   -2.63682e
+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    4.58780e+04   -2.17805e+05    3.12032e+02    1.52337e+02
           Step           Time         Lambda
         500100     1000.20007        0.00000
....................................................................................................................................
My input file:
title               = M2 in dmPC
cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  500000   ; total 1000 ps = 1 ns !
nstcomm             =  1
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
rlist               =  1.2
coulombtype         =  PME
rcoulomb            =  1.2
rvdw                =  1.2
pbc                 =  xyz
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =  Protein  DMPC  SOL  Na
tau_t               =  0.1      0.1   0.1  0.1
ref_t               =  310      310   310  310
; Energy monitoring
energygrps          =  Protein  DMPC  SOL  Na
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  1.0
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  310.0

 

__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com

-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++