[gmx-users] NPT for compressing the system

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 14 20:15:44 CEST 2010

Moeed wrote:
> Hello,
> Thanks for your reply. As for the simulation box, I did not change 
> anything and I am still saying that I am having a cubic box of size 
> 30nm. When I view the molecule in ngmx I see the cubic box.. no problem 
> with that. What I was referring to was the option on menu bar where one 
> can select type of box to view the trajecotry and using say triclinic 
> box I see chain fits better (almost completely)in the box while in the 
> case of cubic (which is my real box) I see molecules is not fitted 
> completely inside the box.. I was just asking why is this happening. as 
> you said "none of that probably means anything" .  I think also it is 
> unnecessary for now so please dont get confused.

As I suspected.  If you have a cubic box, you can certainly change a 
representation in any way you want, but it is meaningless.  You've got a cube, 
plain and simple.

> As you requested I am including ALL the commands I used from the very 
> beginning starting from replicating a 4C unit.
> editconf -f Eth4C.pdb -o Eth4C-d.gro -princ -d 0.058 -bt cubic
> editconf -f Eth4C-d.gro -o Eth4C-d-index.gro -n index.ndx -princ
> genconf -f Eth4C-d-index.gro -o Eth4C-d-index-rep30.gro -nbox 30 1 1  now I have PE chain of 60 units.
> using proper rtp and hdb files:
> pdb2gmx -f
> Eth4C-d-index-rep30-res.gro -o Eth4C-d-index-rep30-res-pdb2.gro -p
> Eth4C-d-index-rep30-res-pdb2.top -ff oplsaa >& output.pdb2gmx
> Then I EM this last gro file but since dimensions are 15 * 0.5 0.5 nm I 
> am getting the error message :
> The cut-off length is
> longer than half the shortest box vector or longer than the smallest
> box diagonal element. Increase the box size or decrease rlist.
> then increased the size >
> editconf -f Eth4C-d-index-rep30-res-pdb2.gro -o Eth4C-d-index-rep30-res-pdb2-boxsize30.gro -box 30 30 30 -angles 90 90 90
> Then I EM the molecule with new box size 30nm and call this energy minimized structure PE60.gro. Now I want to replicate this chain. density demands 1 molecule in 5.76 nm3. As you said I forgot the density for a moment and took a large box.
> PE60 is already in a large enough box (30nm). this is all I did before doing any NPT.
> As for compressing the system to get more realistic structure and approaching the density I am after, I did several NPT runs. All show system is not equilbrated and they all crash and box does not become smaller than 2.2 nm.
> As you proposed I tried doing runs in stepwise manner. Below you see my trails:
> First trial :P 120 bar for 100 ps then P80 bar for 500 ps then P50 for 500 ps. this last run crashes at 2.2 nm size
> As Mark suggested I tried started with lower pressure:
> Second trail: P 50 for 500ps > P40 bar for 500 ps > P35 for 1000ps > P30 for 1000 ps . Below is the results of this last run. before I had negative average Pressure but below the pressure is 30bar and real values fluctuate between -500 to 500 bar. 
> T thermostat is working fine but LJ Columb terms not reaching equilibrium. Also box size is 2.7 nm which is larger than former trials.Molecule in not inside the box for almost the entire simulation.Only a small portion in inside and since it is long can not fit in.

Understand that "inside" and "outside" are completely meaningless terms when 
using periodic boundary conditions.


More problematic is if the molecule is so poorly oriented that it is interacting 
with itself through PBC, leading to spurious forces.  The only way for anyone to 
help you better is probably through posting images.  If you wish to do this, 
please follow the guidelines listed below (point number 3).


> Do i need to start with lower pressures and go to higher values. Because the size is not changing that much with 30 bar?

It seems to me that you may have found a stable state, but perhaps the 
configurations you're getting aren't appropriate (see above).  Hard to say at 
this point.

A different approach might be to simulate for a while first under NVT 
conditions, allowing your PE to collapse in on itself without the box quickly 
compressing around it.  Then try your compression scheme on the structure that 
results from NVT.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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