On 7/19/13 6:55 AM, bipin singh wrote:
Sorry for my silly mistake.
I have a doubt regarding the expected difference in total No. of H-bonds
calculated with whole a MD trajectory (protein+solvent box) and H-bonds
calculated with concatenated frames (only protein) from a MD trajectory.
I mean, will the number of H-bonds present at a particular time in a MD
trajectory (protein+solvent), should be exactly same as number of H-bonds
calculated using trajectory made of concatenated frames (only protein) from
(if we look at number of H-bonds present at same point of time in both).
Because I am not getting the exact match between the two, there is random
difference of 1-3 H-bonds at some point of time.
I suspect that the issue stems from having to manually set the box. I don't
understand why you would have to do this after running a simulation in explicit
solvent. Did you just extract the protein coordinates from the explicit
simulation? If so, I don't see how the box information would be omitted.
You can get spurious H-bonds across PBC if you are manually setting a bad box
size in a given frame or series of frames. Without the exact sequence of
commands from what you have done, it's pure guesswork.
-Justin
On Fri, Jul 19, 2013 at 2:43 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 7/19/13 4:17 AM, bipin singh wrote:
According to the suggestion I added the box to the trajectory using -box
option of trjconv, using the following commands:
trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc
then using the g_hbond on the output trjectory (traj_box.xtc) run
successfully but gives the wrong number of H-bonds between the proteins
atoms.
I have also tried to process the output trajectory (traj_box.xtc) with
trjconv using -pbc mol -ur compact options before using g_hbond, but again
I have got wrong number of H-bonds.
Please help me to rectify the error.
A 0.9-nm cubic box is likely too small to correctly accommodate even an
amino acid, let alone an entire protein.
-Justin
On Fri, Jul 19, 2013 at 11:19 AM, bipin singh <bipinel...@gmail.com>
wrote:
Thanks a lot Prof. David. I will try this.
On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel <
sp...@xray.bmc.uu.se> wrote:
On 2013-07-19 06:26, bipin singh wrote:
Hello all,
I was using g_hbond to calculate H-bonds for a trajectory made from
several
individual snapshots from MD simulation, but because this trajectory
does
not have the coordinates/information for simulation box, g_hbond is
giving
the following error:
Fatal error:
Your computational box has shrunk too much.
g_hbond_mpi can not handle this situation, sorry.
Please let me know, if there is any way to rectify this error.
you can add a box to your trajectory using trjconv.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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Department of Pharmaceutical Sciences
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University of Maryland, Baltimore
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jalem...@outerbanks.umaryland.edu | (410) 706-7441
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