[gmx-users] TPIC and GMX_TPI_DUMP
João M. Damas
jmdamas at itqb.unl.pt
Sat Aug 31 03:54:22 CEST 2013
Sorry, where I said "put it as the last coordinate on the .tpr file you're
building" it should be "put it as the last coordinate of each frame of the
.trr file". You'll need to do some trajectory "hand-editing".
João
On Sat, Aug 31, 2013 at 2:41 AM, João M. Damas <jmdamas at itqb.unl.pt> wrote:
> Oh, you were talking about the Energy Distribution output (-tpid), sorry.
> So, I haven't used much this output, but from what I see, that energies
> histogram is going indefinitely. It seems like a bug in the calculation of
> the energy bins, and my intuition is telling me that it has something to do
> with the volume correction.. Maybe?
>
> My suspicion starts with you saying that you are centering the prosthetic
> group at 0,0,0. That's not the regular procedure for tpi insertions. The
> regular procedure is to center the molecule to insert at 0,0,0. About the
> system, you should calculate the average geometric center of the prosthetic
> group and use it as the center for insertion! (put it as the last
> coordinate on the .tpr file you're building, see the manual). In short: be
> careful with your trjconv command and maintain the integrity of the
> trajectory (PBC, wholeness, for example).
>
> Best,
> João
>
>
> On Sat, Aug 31, 2013 at 1:30 AM, Rafael I. Silverman y de la Vega <
> rsilverm at ucsc.edu> wrote:
>
>> 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
>> > --
>> > gmx-users mailing list gmx-users at gromacs.org
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>
>
>
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
>
--
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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