Dear Dr.Justin<br><br>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>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>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><br>mdrun -v -deffnm umbrella0 -px pullx0.xvg -pf pullf0.xvg -cpi NPT.cpt <br>
<br>what is your point of view now?<br>What do you think if I use NPT.enr OR NPT.trr OR in grompp(especially NPT.enr) ?<br>Because all of information about NPT step are included in this files.<br><br>Thanks in advance for your <br>
<br><div class="gmail_quote">On Sun, May 8, 2011 at 5:47 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;">
<div class="im"><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>
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 ,P=1 bar)<br>
But their values in my umbrela.log files are not as before (for example P=-8.434578e+1)<br>
<br>
Where did I wrong?<br>
</blockquote>
<br></div>
I have no clue. You didn't provide your commands or any evidence that the prior ensemble was to be maintained. If you have done NPT equilibration in each window, then pass the .cpt file to grompp and the ensemble should be preserved in each window. Note that an instantaneous pressure value means nothing, as discussed weekly on 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>
<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>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></blockquote></div><br>