[gmx-users] TPIC and GMX_TPI_DUMP
Rafael I. Silverman y de la Vega
rsilverm at ucsc.edu
Sat Aug 31 02:30:13 CEST 2013
I am centering the insertion on the prosthetic group, which I put as 0 0 0.
I have a 222 amino acid protein, in maybe .2 M NaCl, I parametrized flavin
mononucleotide, which sits inside the protein.
I got the .pdb files written, I was setting the GMX_TPI_DUMP in a different
terminal window. Dumb mistake.
Here is the first 100 lines from the xvg. The lines go on for a LONG way
# This file was created Fri Aug 30 16:54:06 2013
# by the following command:
# mdrun -s tpic.tpr -rerun tpic_in.trr -deffnm tpic -nt 1
#
# mdrun is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@ title "TPI energy distribution"
@ xaxis label "\xb\f{}U - log(V/<V>)"
@ yaxis label "count"
@TYPE xy
@ subtitle "number \xb\f{}U > 50: 1.996e+03"
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "direct"
@ s1 legend "reweighted"
-1445442.50 0 -nan
-1445442.40 0 -nan
-1445442.30 0 -nan
-1445442.20 0 -nan
-1445442.10 0 -nan
-1445442.00 0 -nan
-1445441.90 0 -nan
-1445441.80 0 -nan
-1445441.70 0 -nan
-1445441.60 1 -nan
-1445441.50 0 -nan
-1445441.40 0 -nan
-1445441.30 0 -nan
-1445441.20 0 -nan
-1445441.10 0 -nan
-1445441.00 0 -nan
-1445440.90 0 -nan
-1445440.80 0 -nan
-1445440.70 0 -nan
-1445440.60 0 -nan
-1445440.50 0 -nan
-1445440.40 0 -nan
-1445440.30 0 -nan
-1445440.20 0 -nan
-1445440.10 0 -nan
-1445440.00 0 -nan
-1445439.90 0 -nan
-1445439.80 0 -nan
-1445439.70 0 -nan
-1445439.60 0 -nan
-1445439.50 0 -nan
-1445439.40 0 -nan
-1445439.30 0 -nan
-1445439.20 0 -nan
-1445439.10 0 -nan
-1445439.00 0 -nan
-1445438.90 0 -nan
-1445438.80 0 -nan
-1445438.70 0 -nan
-1445438.60 0 -nan
-1445438.50 0 -nan
-1445438.40 0 -nan
-1445438.30 0 -nan
-1445438.20 0 -nan
-1445438.10 0 -nan
-1445438.00 0 -nan
-1445437.90 0 -nan
-1445437.80 0 -nan
-1445437.70 0 -nan
-1445437.60 0 -nan
-1445437.50 0 -nan
-1445437.40 0 -nan
-1445437.30 0 -nan
-1445437.20 0 -nan
-1445437.10 0 -nan
-1445437.00 0 -nan
-1445436.90 0 -nan
-1445436.80 0 -nan
-1445436.70 0 -nan
-1445436.60 0 -nan
-1445436.50 0 -nan
-1445436.40 0 -nan
-1445436.30 0 -nan
-1445436.20 0 -nan
-1445436.10 0 -nan
-1445436.00 0 -nan
-1445435.90 0 -nan
-1445435.80 0 -nan
-1445435.70 0 -nan
-1445435.60 0 -nan
-1445435.50 0 -nan
-1445435.40 0 -nan
-1445435.30 0 -nan
-1445435.20 0 -nan
-1445435.10 0 -nan
-1445435.00 0 -nan
-1445434.90 0 -nan
-1445434.80 0 -nan
-1445434.70 0 -nan
On Fri, Aug 30, 2013 at 5:19 PM, João M. Damas <jmdamas at itqb.unl.pt> wrote:
> PBC is on works, so the centering is not important. My question had to do
> with the center of insertion: random for tpi, specific for tpic.
>
> That's really my second guess, the infinite energies. The tpi code has a
> way to deal with them internally. Run the insertion [mdrun] with "-debug 1"
> flag and see how many non-finite energies do you hit. Maybe all (number of
> frames times the number of insertions?
>
> Can you post 100 lines or so of your .xvg file? I'm curious about it. Maybe
> 4.6.3 has some new output I'm unaware of.
>
> Also, can you tell something more about your system?
>
> Best,
> João
>
>
> On Sat, Aug 31, 2013 at 12:55 AM, Rafael I. Silverman y de la Vega <
> rsilverm at ucsc.edu> wrote:
>
> > Thanks for the reply João,
> > I am using gromacs 4.6.3, I did centre all 4 frames at the prosthetic
> > group.
> > I tried GMX_TPI_DUMP = 5.0e+3, 5.0e+20, and even 5.0e-03, still, not a
> > single .pdb file written.
> > I am doing this on a 4 frame trajectory, consisting of ~7000 atoms per
> > frame. I think it may have to do with the frames that have infinite
> > chemical potential with the insertion? It doesnt seem to have anything to
> > do with TPI_DUMP, when I lower rtpi to 0.05 the .xvg file becomes less
> > ridiculously large, only 0.5 gigs...
> > I suppose I need to try an older version of gromacs, and see if my setup
> > works there
> > --
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>
>
>
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
> --
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