[gmx-users] TPIC and GMX_TPI_DUMP
Rafael I. Silverman y de la Vega
rsilverm at ucsc.edu
Sat Aug 31 04:31:58 CEST 2013
Thanks!
I will try these latest suggestions!
On Fri, Aug 30, 2013 at 7:27 PM, Rafael I. Silverman y de la Vega <
rsilverm at ucsc.edu> wrote:
> Yes, I hand edited the .tpr file to get the thing to work, otherwise I got
> errors with particle numbers being different.
>
>
> On Fri, Aug 30, 2013 at 6:54 PM, João M. Damas <jmdamas at itqb.unl.pt>wrote:
>
>> 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
>> >> > > --
>> >> > > gmx-users mailing list gmx-users at gromacs.org
>> >> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> > > * Please search the archive at
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>> posting!
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>> >> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >> > >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > João M. Damas
>> >> > PhD Student
>> >> > Protein Modelling Group
>> >> > ITQB-UNL, Oeiras, Portugal
>> >> > Tel:+351-214469613
>> >> > --
>> >> > gmx-users mailing list gmx-users at gromacs.org
>> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> > * Please search the archive at
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>> >> >
>> >> --
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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
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
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>>
>
>
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