On 29/10/2010 5:48 PM, vinothkumar mohanakrishnan wrote:
Hi Gromacians
I want to do equilibration of water (spc model) first in the NVT
ensemble and then in the NPT ensemble to maintain a temperature of
300K and a pressure of 1 bar respectively. The NVT equilibration works
fine and the average temperature turns out to be 299.229 K.
Energy Average RMSD Fluct.
Drift Tot-Drift
------------------------------
-------------------------------------------------
Temperature 299.229 10.3092 10.2463
0.0393873 3.93877
Heat Capacity Cv: 12.494 J/mol K (factor = 0.00118698)
when i do NPT equilibration i am not getting the desired pressure as
1 bar or atleast close to 1 bar (between 1-1.4 bar). In the mdp file i
used semiisotropic pressure coupling type because i want to fix the
length of the box same on two axis as that of the original box size
and want to change it only on one axis. can any one tell me why iam
not getting the desired pressure of 1 bar?.
This looks normal for a smallish water system over 100ps. See
http://www.gromacs.org/Documentation/Terminology/Pressure
Mark
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Pressure (bar) 7.4339 574.052 573.574
0.812129 81.2138
Given below is my mdp file (NPT equilibration). any help is highly
appreciated.
title = DCE NVT equilibration
cpp = usr/bin/cpp
integrator = md
nsteps = 100000
dt = 0.001
nstxout = 100
nstvout = 100
nstenergy = 100
nstlog = 100
ns_type = grid
nstlist = 1
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.0
pme_order = 4
fourierspacing = 0.16
pbc = xyz
tcoupl = V-rescale
tc-grps = system
tau_t = 0.1
ref_t = 300
pcoupl = berendsen
pcoupltype = semiisotropic
tau_p = 0.5
ref_p = 1.0 1.0
compressibility = 0.0 4.5e-5
DispCorr = Enerpres
gen_vel = yes
gen_temp = 300
gen_seed = 173529
Regards
Vinoth
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