[gmx-users] Re: NPT issue in 4.0.7 and 4.5.3

xiaowu759 xiaowu759 at qq.com
Thu Apr 14 02:49:38 CEST 2011


Dear Moeed,
   You seem to be encountering same problem to mine, which was posted to this list, .titled "Unexpected results arising from T- and P-coupling methods". Some gmxers responded it. You can look for and see them. I wish they can be helpful to deal with your problem.
  
 Chaofu Wu, Dr.
  ------------------
 
Date: Wed, 13 Apr 2011 20:22:02 -0400
From: Moeed <lecielll at googlemail.com>
Subject: [gmx-users] NPT issue in 4.0.7 and 4.5.3
To: gmx-users at gromacs.org
Message-ID: <BANLkTimHFgwpUy6V5OGkAi_JBS2OzfwsQA at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hello,

I have run 2 ns simulations on a hydrocarbon system (initial density of ~ 2
SI and box size is 15 nm), one with version 4.0.7 and the other trial using
4.5.3. Both runs are almost equilibrated to 70 bar pressure but one is
giving density of above 600SI (4.0.7) and the other density of around 15 SI
(4.5.3). With 4.5.3 applying 100 bar pressure does not comrades the system
either to the desired density. I need to study the system at different
pressures from 1 to 70 bar, and I am wondering if the system can not be
compressed with these ref_p values how can I keep the pressure fixed at P <
70 bar!?

Please help if you have any idea on why these two versions are giving
inconsistent results and which one is reliable.

Thanks so much,


4.0.7

Statistics over 250001 steps [* 1500.0001 thru 2000.0001 ps ],* 14 data sets
The term 'Cons. rmsd ()' is averaged over 2501 frames
All other averages are exact over 250001 steps

Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift
-------------------------------------------------------------------------------
Angle                       36.9945   0.806738   0.804483  0.0521993
0.208798
Ryckaert-Bell.              9.04227   0.376253   0.371412  0.0521057
0.208424
LJ-14                       5.23048   0.119612   0.119611 0.00033983
0.00135933
Coulomb-14                 -1.66329   0.104171   0.102175  0.0175753
0.0703015
LJ (SR)                    -27.3967          0          0  0.0421934
0.168774
Coulomb (SR)                8.98711   0.163579    0.16062 -0.0268199
-0.10728
Potential                   31.1944          0          0   0.137594
0.550377
Kinetic En.                 51.1009   0.987759   0.987724 0.00725949
0.0290381
Total Energy                82.2953          0          0   0.144851
0.579408
Temperature                  299.98    5.79849    5.79828 0.000340897
0.170449
*Pressure (bar)              69.3587    414.279    414.256  0.0298385
14.9193*
Cons. rmsd ()            4.01744e-06 1.41883e-07 1.41883e-07
0          0
*Box-X                       3.04882          0          0 3.57512e-06
0.00178757
Box-Y                       3.04882          0          0 3.57512e-*


-----------------------------
4.5.3.

[* 1500.0001 thru 2000.0001 ps ],*

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Angle                       37.1357      0.071   0.812307  -0.099711
(kJ/mol)
Ryckaert-Bell.              9.17677       0.14   0.445934  -0.529281
(kJ/mol)
LJ-14                       5.18878     0.0087   0.137673   -0.03119
(kJ/mol)
Coulomb-14                 -1.60372      0.051   0.126405  -0.144403
(kJ/mol)
LJ (SR)                    -4.24478       0.29   0.742141   0.697187
(kJ/mol)
Coulomb (SR)                8.97451      0.082   0.198278   0.232025
(kJ/mol)
Potential                   54.6272       0.31    1.20733   0.124627
(kJ/mol)
Kinetic En.                 51.1047      0.021     0.9945  -0.066306
(kJ/mol)
Total Energy                105.732       0.31    1.58869   0.058321
(kJ/mol)
Temperature                 300.002       0.12    5.83806  -0.389239  (K)
*Pressure                     66.734        5.3      91.83    11.5294  (bar)
*
Constr. rmsd             2.2661e-10    2.3e-10 3.58302e-08 -1.3595e-09  ()
*Box-X                       11.0055      0.082   0.175309  -0.496198  (nm)
Box-Y                       11.0055      0.082   0.175309  -0.496198  (nm)*






pbc              =  xyz

integrator          =  md
dt                  =  0.002
nsteps              =  1000000
nstcomm             =  100
nstenergy           =  100
nstxout             =  100

nstlist             =  10
ns_type             =  grid

coulombtype         =  Shift
vdw-type            =  Shift
rcoulomb-switch     =  0
rvdw-switch         =  0.9
rlist               =  1.2
rcoulomb            =  1.2
rvdw                =  1.0

Tcoupl              =  v-rescale
tc-grps             =  System
tau_t               =  0.1
ref_t               =  300


Pcoupl              =  berendsen
Pcoupltype          =  isotropic
tau_p               =  1
compressibility     =  4.5e-5 4.5e-5
ref_p               =  70


gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529


constraints             = all-bonds
constraint-algorithm = lincs
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