<div dir="ltr">Hi Justin,<br>Thank you very much for your quick reply.... It is really encouraging to get such response<br>For the answer of third question, How can I assign different random velocity ?<br>Is it like assigning the different force-field ?<br>
Please elaborate or suggest some reference if you can ?<br><br><br>With Thanks,<br>Vivek<br><br><div class="gmail_quote">2008/9/10 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d"><br>
<br>
vivek sharma wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Everybody,<br>
<br>
I am running MD simulation for getting various conformation of a molecule, that can act as better receptor for docking purpose.<br>
While doing so, I got a number of doubts.<br>
Firstly what should be the range of time step I can keep in .mdp file (right now I am using .002 ps of time step, Can I increase it further ?)<br>
</blockquote>
<br></div>
That depends largely on your force field and whether or not you're applying constraints. For protein simulations (with constraints), 1-2 fs is pretty standard; some UA lipid simulations use 4-5 fs.<div class="Ih2E3d">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
My second question is for how long I should run my simulation to get various conformation (or what is the time interval that can be taken as in general after which biomolecule can change their conformation ?)<br>
</blockquote>
<br></div>
There is no simple answer to this question. Sampling is always an issue in MD. Some conformational changes occur on the nanosecond timescale, others in excess of several hundred ns, or even a few microseconds! Perhaps your system alters its conformation rapidly, such that changes can be observed in a few ns, but that is for you to determine :)<div class="Ih2E3d">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
How should I pick up various conformation from the mdrun that can make a sense ?<br>
<br>
</blockquote>
<br></div>
Probably the best idea (IMHO) is to run several simulations, each starting from different random velocities. Run each for the same length of time and compare the results. Do all the simulations wind up giving you the same thing? Are there substantial differences in the conformations?<br>
<br>
As for extracting conformations along a trajectory (using trjconv -dump), this may or may not be relevant. What if a certain conformation occurs once for a single frame in one trajectory, but never again in ten other trajectories? Do you care about that frame? Probably not, based on reasonable sampling. What if a certain conformation occurs a few times over a few trajectories? How do you determine its relevance? Such are the challenges of simulation.<br>
<br>
You can use g_cluster to do RMSD clustering to determine which conformations are similar along the trajectory. Whether or not any of these "make sense" is entirely up to you and what you know about your system :)<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">
I know the questions are not strictly related to gromacs. my apologies for putting such questions.<br>
<br>
If anybody has insight into these questions, please reply.<br>
<br>
<br>
With Thanks,<br>
Vivek<br>
<br>
<br></div>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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