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<html><head><title>Re[6]: [gmx-users] Non-conservation of total energy while using structure file to resume the simulation</title>
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<p>Hi, Tsjerk.</p>
<p><br></p>
<p>Thanks for your help.</p>
<p><br></p>
<p><span class=rvts6>> Try</span></p>
<p><br></p>
<p><span class=rvts6>> editconf -f your_run_input_file.tpr -o test.gro</span></p>
<p><br></p>
<p><span class=rvts6>> to see if the box is stored correctly in the .tpr. Alternatively, you</span></p>
<p><span class=rvts6>> can do gmxdump -s your_run_input_file.tpr, and browse for the box in</span></p>
<p><span class=rvts6>> the output. </span></p>
<p>Yea, both tests show "zero" box right in .tpr file!</p>
<p><br></p>
<p><span class=rvts6>> Then, see if you can reproduce the problem with the last</span></p>
<p><span class=rvts6>> frame of the .trr file extracted, </span></p>
<p>I'm afraid I cannot do it quickly... </p>
<p>For the future: I used double-precision mode, </p>
<p>how much should be the precision (-ndec) of the extracted frame? </p>
<p><br></p>
<p><span class=rvts6>> and consider submitting a bugzilla.</span></p>
<p>Sure. </p>
<p><br></p>
<p><span class=rvts6>> Cheers,</span></p>
<p><br></p>
<p><span class=rvts6>> Tsjerk</span></p>
<p><br></p>
<p><span class=rvts6>> On Wed, Jun 9, 2010 at 8:54 AM, Dmitri Dubov <</span><a class=rvts7 href="mailto:ddubov@ngs.ru">ddubov@ngs.ru</a><span class=rvts8>> wrote:</span></p>
<p><span class=rvts9>>> First, sorry for the revival of this thread so late (maybe it should be</span></p>
<p><span class=rvts9>>> better to start a new one).</span></p>
<p><br></p>
<p><span class=rvts6>>>> ----- Original Message -----</span></p>
<p><br></p>
<p><span class=rvts6>>>> From: Dmitri Dubov <</span><a class=rvts7 href="mailto:ddubov@ngs.ru">ddubov@ngs.ru</a><span class=rvts8>></span></p>
<p><br></p>
<p><span class=rvts6>>>> Date: Thursday, May 27, 2010 19:11</span></p>
<p><br></p>
<p><span class=rvts6>>>> Subject: Re[2]: [gmx-users] Non-conservation of total energy while</span></p>
<p><br></p>
<p><span class=rvts6>>>> using structure file to resume the simulation</span></p>
<p><br></p>
<p><span class=rvts6>>>> To: Discussion list for GROMACS users <</span><a class=rvts7 href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><span class=rvts8>></span></p>
<p><br></p>
<p><span class=rvts9>>>>> > I expect that either</span></p>
<p><br></p>
<p><span class=rvts9>>>>> > grompp -f new -o newtpr</span></p>
<p><br></p>
<p><span class=rvts9>>>>> > mdrun -s newtpr -cpi old_state.cpt</span></p>
<p><br></p>
<p><span class=rvts9>>>>> No, this way is unsuccessful, maybe due to somewhat contradictive</span></p>
<p><span class=rvts9>>>>> instructions:</span></p>
<p><br></p>
<p><span class=rvts9>>>>> grompp supplies newtpr with usual options</span></p>
<p><br></p>
<p><span class=rvts9>>>>> tinit = 0</span></p>
<p><br></p>
<p><span class=rvts9>>>>> nsteps = 100000</span></p>
<p><br></p>
<p><span class=rvts9>>>>> simulation_part = 1</span></p>
<p><br></p>
<p><span class=rvts9>>>>> and from old_state.cpt the system finds itself on 100000th step already</span></p>
<p><span class=rvts9>>>>> and stops.</span></p>
<p><br></p>
<p><span class=rvts6>>>> OK. Presumably some more cunning choice of .mdp options would work,</span></p>
<p><br></p>
<p><span class=rvts6>>>> or using grompp, tbconv -extend and then mdrun.</span></p>
<p><br></p>
<p><span class=rvts9>>>>> > grompp -f new -t old_state.cpt -o newtpr</span></p>
<p><br></p>
<p><span class=rvts9>>>>> > mdrun -s newtpr</span></p>
<p><br></p>
<p><span class=rvts9>>>>> > will do what you want. Please report back if one or both work :-)</span></p>
<p><br></p>
<p><span class=rvts9>>>>> And the latter variant is working! More precisely I use</span></p>
<p><br></p>
<p><span class=rvts9>>>>> grompp -f new -t old_state.cpt -c oldtpr -o newtpr</span></p>
<p><br></p>
<p><span class=rvts9>>>>> mdrun_d -s newtpr</span></p>
<p><br></p>
<p><span class=rvts6>>>> Mark</span></p>
<p><br></p>
<p><span class=rvts9>>> But I have noted just now that using grompp with -t option results in some</span></p>
<p><span class=rvts9>>> bug: after simulation right size of my cubic box (last line of input</span></p>
<p><span class=rvts9>>> structure file)</span></p>
<p><br></p>
<p><span class=rvts9>>> 10.00000 10.00000 10.00000</span></p>
<p><br></p>
<p><span class=rvts9>>> changes in confout.gro to meaningless</span></p>
<p><br></p>
<p><span class=rvts9>>> 0.00000 0.00000 0.00000</span></p>
<p><br></p>
<p><span class=rvts9>>> To analyse the output properly (e.g. with g_rdf tool) I have to correct this</span></p>
<p><span class=rvts9>>> line manually.</span></p>
<p><br></p>
<p><span class=rvts9>>> And I'm worried whether this bug effects to my simulation itself, during md</span></p>
<p><span class=rvts9>>> integration of NVE ensemble in vacuum?</span></p>
<p><br></p>
<p><span class=rvts11>-- </span></p>
<p>Regards<span class=rvts11>,</span></p>
<p><span class=rvts11> Dmitri </span></p>
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