Amjad Farooq wrote:
Hello Justin,
Thank you for your insights into the g_dist command. I am becoming quite
an expert on it now!
I have another question for you and other GROMACS users:
I am doing MD simulation on a protein(35aa)-peptide(12aa) complex and I
noticed spikes in backbone RMSD roughly half way into my 10-ns
trajectory (please see the attached image). The experimentally measured
Kd for this protein-peptide complex is around 100uM, so this complex
should not be expected to be very stable but what are those spikes? Do
they mean anything or is there something wrong with my MD setup? Please
shed light.
You haven't properly corrected for periodicity.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-Justin
Thank you all!
Amjad
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Amjad Farooq <amjadfar...@yahoo.com>; Discussion list for GROMACS
users <gmx-users@gromacs.org>
*Sent:* Thursday, June 30, 2011 1:54 PM
*Subject:* Re: [gmx-users] Calculate distance between two atoms
Amjad Farooq wrote:
> Hello everyone,
>
> I would like to calculate distance between two atoms from an MD run.
For example, how do I probe changes in distance between CD atom of Pro23
and OE1 atom of Glu75 as a function of simulation time.
>
> From the manual, I understand that one should use the command g_dist
that includes the index.ndx file. My questions are:
>
> (1) How do I create an index.ndx file for the the above-mentioned
pair of atoms?
Use make_ndx. Type 'help' at the prompt for examples. For indices with
just one atom each this is not strictly necessary; you can create the
necessary groups with a text editor.
> (2) What is the exact format of g_dist that should be applied on the
command line?
>
Please read g_dist -h.
-Justin
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------------------------------------------------
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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