<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><br><span></span></div><div><span>Just curious. what is inside .cpt file,is there a way I can change it in readable format?</span></div><div><span>I also notice that every mdrun step I got a state.cpt and state_prev.cpt as well, any difference between the two?</span></div><div><span>And using .cpt seems a little faster (a couple of hours or so) than without using it for the same time length simulation, do you happen to know the reason?</span></div><div><br><span></span></div><div><span>Thanks,</span></div><div><br><span></span></div><div><span>yao</span></div><div><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Arial" size="2"><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 11:28 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>> Ok, I see the problem. Like your tutorial, I used cpt for NVT/NPT to mdrun/continue NVE production run.<br>> 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.<br>> Am I supposed to do so if I wanna simulate NVE?<br>> <br><br>NVE will keep the energy constant under the set conditions. I do not know why P is constant; with V being constant (by definition), P should fluctuate under NVE. Providing a .cpt file
from a previous NVT or NPT will define the conditions under which NVE is run (i.e. what energy is to be maintained).<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>><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 10:42 AM<br>> *Subject:* Re: [gmx-users] where are Density and Volume?<br>> <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>> > *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:* 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 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>> <mailto:<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>> <mailto:<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>>
<mailto:<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
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><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>
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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>> <mailto:<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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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>> <mailto:<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>> >
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<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.
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