<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hi, Justin</span></div><div><span><br></span></div><div><span>Ok, I see the problem. Like your tutorial, I used cpt for NVT/NPT to mdrun/continue NVE production run.</span></div><div><span>So though I did not set V or P constraint in NVE mdp, it still keeps them as constant, like my NVE did not work.</span></div><div><span>Am I supposed to do so if I wanna simulate NVE?</span></div><div><span><br></span></div><div><span>Thanks,</span></div><div><span><br></span></div><div><span>Yao</span></div><div><br></div><div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><font size="2" face="Arial"><hr size="1"><b><span style="font-weight:bold;">From:</span></b> Justin A. Lemkul
<jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Thursday, October 13, 2011 10:42 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] where are Density and Volume?<br></font><br>
<br><br>Yao Yao wrote:<br>> Hi Justin,<br>> <br>> thanks,<br>> <br>> that is just initial value, no fluctuation over time.<br>> <br><br>Right. The volume is constant, therefore the initial values of density and volume are always the same.<br><br>-Justin<br><br>> yao <br>> ------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Thursday, October 13, 2011 10:24 AM<br>> *Subject:* Re: [gmx-users] where are Density and Volume?<br>> <br>> <br>> <br>> Yao Yao wrote:<br>> > Hi Justin,<br>> ><br>> > It is NVE. Is there a consistent way I can know my D and
V?<br>> ><br>> <br>> Then you've got the same case as NVT (for these values, anyway) - volume and density are fixed at whatever value they started at. editconf should have printed this somewhere along the way.<br>> <br>> -Justin<br>> <br>> > Thanks,<br>> ><br>> > Yao<br>> ><br>> > ------------------------------------------------------------------------<br>> > *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> <mailto:<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>><br>> > *To:* Yao Yao <<a ymailto="mailto:yao0o@ymail.com" href="mailto:yao0o@ymail.com">yao0o@ymail.com</a> <mailto:<a ymailto="mailto:yao0o@ymail.com" href="mailto:yao0o@ymail.com">yao0o@ymail.com</a>>>; Discussion list for GROMACS users <<a
ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br>> > *Sent:* Thursday, October 13, 2011 9:58 AM<br>> > *Subject:* Re: [gmx-users] where are Density and Volume?<br>> ><br>> ><br>> ><br>> > Yao Yao wrote:<br>> > > Hi,<br>> > ><br>> > > I wanna get Density and Volume of my system after simulation.<br>> > > I found in tutorials by Justin and kerrigan?, that g_energy -f *.edr -o should work,<br>> > > but I do not find in my version 4.5.1 and 4.5.4. That is kind of weird.<br>> > ><br>> ><br>> > Was it an NVT simulation? If so, those terms are not written
because they are, by definition, constant.<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>> > jalemkul[at]vt.edu | (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>> ><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]vt.edu | (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>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">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
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Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (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>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">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"
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VA<br>> > jalemkul[at]vt.edu | (540) 231-9080<br>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> ><br>> > ========================================<br>> ><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]vt.edu | (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>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org"
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========================================<br>> ><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]vt.edu | (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>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">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 ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">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>> <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]vt.edu | (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>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">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 ymailto="mailto:gmx-users-request@gromacs.org"
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