[gmx-users] NPT for compression

[Mark Abraham]

On 14/07/2010 6:40 AM, Moeed wrote:
> 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 ?
http://www.gromacs.org/Documentation/Terminology/Pressure
> 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?
We can't really tell, because we can't see what data you're basing this 
assessment on. My first guess is that you were looking at a PDB file, 
and 22A is around 2nm.

"Simulation stops"? What does that mean?
>
>
> 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*

All this means is that over the course of the simulation the observed 
pressure was negative - which is what you expect for a system that got 
dramatically smaller, and then wasn't allowed to equilibrate under more 
normal pressure-coupling.

> 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).

Yes, it's almost certainly not equilibrated. You've coerced a serious 
change to the conformation in an eyeblink. Give it some time under 
normal conditions :-)

> 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?
You do not want (or need) to use the same groups for T-coupling and 
energy monitoring. Under normal circumstances, GROMACS default 
definitions for protein and SOL just work. Under your circumstances, 
they probably won't. So, use make_ndx to make your polymer group, and, 
if appropriate, a hexane group. Then T-couple to SOL, polymer and 
hexane. If they're small, it might be more appropriate to merge hexane 
and/or polymer into one of the other groups.

If you're really sure you want to monitor energies on subsets of the 
hexane group, then go and make those subsets.

Mark
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