Thanks!
I will try these latest suggestions!
On Fri, Aug 30, 2013 at 7:27 PM, Rafael I. Silverman y de la Vega <
rsilv...@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
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 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 las
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 wrote:
> Oh, you were talking
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
wi
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 mi
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 s
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
Dear Rafael,
Which version of GROMACS are you using? I cannot guarantee my following
comments are valid in 4.6.X, only on 4.0.X and 4.5.X.
What values have you tried from GMX_TPI_DUMP? Basically, the value you set
it to will be the energy value that will be compared with the epot of the
system wi
Hi all,
I am trying to insert a water into a prosthetic group binding cavity. I
cant seem to get an output .pdb file of the insertions, I set GMX_TPI_DUMP
in my shell with $ export GMX_TPI_DUMP=xxx but no numbers seemed to work. I
cant really get good information out of the .xvg output either, it a
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