[gmx-users] NPT for compression

[Moeed]

Hello,

I followed the hints. I did several NPT runs and I found out pressure above
100 eg 120 bar gives final boxsize close to volume of box I want. But I dont
know why pressure given by g_energy is totally different.

1- I looked at values in xvg file and I notoced pressre starts froma very
low value, also takes negative and postive values. If I am doing NPT why P
is changing ?
2- at the end of xvg file I see final dimensions are 2*2*2 . Also I checked
the size in ngmx and I see that long chain is compressing very nicely and
takes a very convoluted conformation in a very small size. I selected 1000
ps but after 727 ps simulation stops (it seems box size can not be reduced
further).However, When I open the gro file PE60_after_MD dimensions are
22*22*22! :( why is this happening?


Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift
-------------------------------------------------------------------------------
Angle                       725.016    41.3878    36.4581  0.0790551
67.8611
Ryckaert-Bell.              231.804     29.096     25.866  0.0537685
46.155
LJ-14                       161.418    8.09535    7.98175 0.00545371
4.68147
Coulomb-14                 -87.8111    8.74814    7.24162  0.0198065
17.0019
LJ (SR)                    -145.619    82.9315     38.527  -0.296365
-254.401
Coulomb (SR)                190.015    14.0939    11.1829 -0.0346165
-29.7149
Potential                   1074.82    73.9367     60.258  -0.172898
-148.416
Kinetic En.                 899.733    29.9816    29.9813 0.000554359
0.475863
Total Energy                1974.56     67.628    52.4374  -0.172344
-147.94
Temperature                 299.757    9.98875    9.98864 0.000184692
0.15854
*Pressure (bar)             -1.43379    141.354    141.205 -0.0261305
-22.4305*
Cons. rmsd ()            5.12607e-06 4.18181e-07 3.98738e-07 5.08597e-10
4.3658e-07
Box-X                       10.7454     7.6259    2.33711 -0.0292936
-25.1457
Box-Y                       10.7454     7.6259    2.33711 -0.0292936
-25.1457
Box-Z                       10.7454     7.6259    2.33711 -0.0292936
-25.1457
Density (SI)                32.6368    57.0897    38.1186   0.171508
147.222
pV                         -5.00443    428.488    428.332 -0.0466916
-40.0802
Vir-XX                      321.928    424.592    424.396   0.051996
44.6335
Mu-X                     0.00138297    0.33292   0.332911 -9.74152e-06
-0.00836214
Lamb-System                 1.00002 0.000363012 0.000363011 -3.17825e-09
-2.72822e-06
Heat Capacity Cv:      12.4926 J/mol K (factor = 0.00111041)

3- The systems seems not to be equilibrated yet. eg LJ SR remains constant
for a while and goes down and its not reaching a plateau after 720 ps (where
simulation stops).

4- When I choose p 200bar , compression continues till 420 ps. Actually
chain takes a specific conformation in such a way that it can not get
compressed further and simulation stops even before former trial (p 120
bar).
a simple question:
5- About tc groups in mdpfile: actually I see people having names like
protein SOL as their groups but I am wondering how I can set the name
"polymer". I thought this comes form the [system] or [molecule] in top file
but its not so (or thought may names are coming form index file). If I want
to add hexane to PE and calculate energies I need to have these two groups
separately. for PE I have three residues Eth EthB EthE.Could you please tell
me how can I include them in one single group 'Polymer"? and use this name
in mdp file?

Thanks for your help.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100713/e2fabcdf/attachment.html>