Dear Dr.Justin<br><br>Thank you for your complete explanation.<br>Please let me discribe where is NPT.cpt comes from:<br><br>Before doing Pulling step,I did an NPT step (as your tutorial) to generate NPT ensemble.<br>the outputs of this step were NPT.cpt, NPT.gro and NPT.enr and ...<br>
<br>Then I used NPT.gro for Pulling step to generate config0.gro and ...<br><br>After this step I used the NPT.cpt and config0.gro and .... to generate umbrella0.tpr with grompp.<br>I think it is obvious now ,where is NPT.cpt come from!<br>
<br>I think my mistake is as you noted.I didn't use any -t option in grompp,Then I lost the information for npt ensemble.<br><br>What do you think<br>Thanks in advance for your reply <br><br><br><br><br><div class="gmail_quote">
On Sun, May 8, 2011 at 7:03 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Dr.Justin<br>
<br><div class="im">
I didn't any equilibration for any windows! Because:<br>
As I know the thermodynamics of the system had wroten in NPT.cpt file (for example the velocities and etc).<br>
</div></blockquote>
<br>
Then where does NPT.cpt come from? Presumably, if you have this file, you did some equilibration. I don't understand what you've done. If you want to rely on previous, equilibrium dynamics under an NPT ensemble, you must do equilibrium MD (not steered) for each configuration under the desired conditions, then pass the .cpt file to grompp -t when building the umbrella sampling input files.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Then when I use that in grompp for each windows ,I expect the same characteristics of system as before(At least the same T)!<br>
<br>
</blockquote>
<br></div>
With "gen_vel = no" and no record of the prior state, this is not a reasonable expectation. You will get a temperature based on the initial forces present in the system (which determine initial velocities). The resulting temperature may or may not be identical to the previous state, but under the influence of a thermostat, you will reach the desired temperature.<br>
<br>
If you're attempting to follow my tutorial directly, at this point I think you should stop and consider the discussion I have in the tutorial on maintaining the ensemble:<br>
<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html</a><br>
<br>
In the example system (one I know very well), it was satisfactory to simply use<br>
"gen_vel = no" and allow these initial forces to govern the resulting dynamics. In many other cases (probably most), you should:<br>
<br>
1. Generate your configurations (SMD, etc)<br>
2. Run individual NPT simulations (or whatever ensemble) for each desired starting configuration (and thus obtain npt0.cpt, npt1.cpt, etc)<br>
3. Initiate umbrella sampling windows using the npt*.cpt files from each window.<br>
<br>
Otherwise, skip step 2, use "gen_vel = yes" and discard the first few hundred ps as equilibration in each window.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Actually after PULLING step I used the following commands:<br>
grompp -f umbrella.mdp -c config0.gro -p complex.top -o umbrella0.tpr -n index.ndx <br>
mdrun -v -deffnm umbrella0 -px pullx0.xvg -pf pullf0.xvg -cpi NPT.cpt<br>
<br>
what is your point of view now?<br>
</blockquote>
<br></div>
These commands do not necessarily preserve the ensemble. Without providing suitable information to grompp -t, the initial state is lost. I still don't know where NPT.cpt comes from. You say you're running grompp immediately after pulling, which is a non-equilibrium ensemble that you don't want to preserve as input into umbrella sampling. That, and likely the settings in SMD vs. US are different, so if NPT.cpt corresponds to your SMD simulation, you probably don't want to be using that for all your umbrella sampling windows, as the information it contains is for one single snapshot somewhere along the SMD run. If this is not the case, and you've generated NPT.cpt in some other manner, you will have to explain where it came from.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
What do you think if I use NPT.enr OR NPT.trr OR in grompp(especially NPT.enr) ?<br>
</blockquote>
<br></div>
Not necessary. Using .cpt files is more accurate.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Because all of information about NPT step are included in this files.<br>
<br>
</blockquote>
<br></div>
Note entirely. The differences between using .edr + .trr vs. .cpt alone are very small, but using a .cpt file is the most rigorously correct way to maintain the ensemble.<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="im">
Thanks in advance for your<br>
<br></div><div><div></div><div class="h5">
On Sun, May 8, 2011 at 5:47 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
mohsen ramezanpour wrote:<br>
<br>
Dear Dr.Justin<br>
<br>
Regarding doing umbrella sampling:<br>
I used gen_vel =no<br>
and I prefer to use from thermodynamics of system in NPT.cpt<br>
<br>
Although the T and P were as I did set in NPT.mdp file (T=310<br>
,P=1 bar)<br>
But their values in my umbrela.log files are not as before (for<br>
example P=-8.434578e+1)<br>
<br>
Where did I wrong?<br>
<br>
<br>
I have no clue. You didn't provide your commands or any evidence<br>
that the prior ensemble was to be maintained. If you have done NPT<br>
equilibration in each window, then pass the .cpt file to grompp and<br>
the ensemble should be preserved in each window. Note that an<br>
instantaneous pressure value means nothing, as discussed weekly on<br>
this list and online:<br>
<br>
<a href="http://www.gromacs.org/Documentation/Terminology/Pressure" target="_blank">http://www.gromacs.org/Documentation/Terminology/Pressure</a><br>
<br>
It is the average that is most meaningful.<br>
<br>
-Justin<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<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>
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