I've missed a part of the previous message, see below:
On 12 November 2013 14:11, Thomas Evangelidis <tevang3.gmail.com> wrote:
> Brian & Pawel,
>
> Thanks for the information. I have done a simulation with a truncated
> octahedron in the past in NAMD using AMBER .prmtop/.inpcrd, but that case
> was easier due to solvateOct LeAP command.
>
> This time I create a protein-membrane-water system as a hexagona prism
> with CHARMM-GUI, I modified the file as described in the tutorial and
> passed it to LeAP. There I did:
>
>
setBox complex centers
,but the box a,b,c vectors were overestimated, so I visually inspected the
periodic cells in VMD and adjusted a,b,c to values given below. I also set
IFBOX to 3 inside .prmtop. By the way, I know what 0,1 and 2 do, but what
does IFBOX==3 mean?
> Regarding the last line of .inpcrd, it seem that VMD perceives the lattice
> vector angles differently. According to this post:
>
> http://archive.ambermd.org/200907/0035.html
>
> the last .inpcrd line correspond to "a b c alpha beta gamma". However, VMD
> definition of alpha, beta and gamma is not exactly as in AMBER. See the
> example below which shows the impact of NPT equilibration with NAMD were
> the protein was constrained:
>
>
> ## last .inpcrd line: 106.0000000 106.0000000 86.0000000 90.0000000
> 90.0000000 120.000000
> # box info at the beginning:
> % molinfo top get {a b c}
> 106.000000 106.000008 87.000000
> % molinfo top get {alpha beta gamma}
> 90.000000 90.000000 60.000004
>
> # box info at the end:
> % molinfo top get {a b c}
> 97.726463 98.022034 76.186539
> % molinfo top get {alpha beta gamma}
> 90.000000 90.000000 60.099697
>
> ## last .inpcrd line: 106.0000000 106.0000000 86.0000000 60.0000000
> 90.0000000 90.000000
> # box info at the beginning:
> % molinfo top get {a b c}
> 106.000000 106.000008 87.000000
> % molinfo top get {alpha beta gamma}
> 90.000000 90.000000 60.000004
>
> # box info at the end:
> % molinfo top get {a b c}
> 95.999474 95.565758 79.677513
> % molinfo top get {alpha beta gamma}
> 90.000000 90.000000 59.849758
>
>
> As I can judge from the above results, "106.0000000 106.0000000
> 86.0000000 90.0000000 90.0000000 120.000000" is equivalent to
> "106.0000000 106.0000000 86.0000000 60.0000000 90.0000000 90.000000",
> namely both Pawel and http://ambermd.org/namd/namd_amber.html are correct.
>
> I have uploaded snapshots of the system in the a-b plane before and after
equilibration. It seems tome that the starting and final position are
identical using both angle sets.
https://www.dropbox.com/sh/i3f3y8xshbfkvy7/V7eSX2Cbr2
Does anyone know the reason for the discrepancy in alpha,beta,gamma angles
between VMD and AMBER (.inpcrd)?
What variables should I monitor to see if I am simulating a correctly
defined periodic system?
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Received on Tue Nov 12 2013 - 04:30:03 PST
